The MED12 NM_005120.3:c.131G>A (NP_005111.2:p.(Gly44Asp)) missense variant has previously been reported in somatic cancers (COSMIC; COSV61329353, n = 856 times), and lies in a statistically significant hotspot (cancerhotspots.org). Experimental evidence: Exact p.Gly44Asp showed reproducibly reduced Cyclin C/CDK8/CDK19 binding (AP-MS n=3) and independent cellular signaling abnormalities versus wild type. Based on available guidelines, this variant is considered to be Likely Pathogenic.
Five-step scale from benign to pathogenic. This variant is likely pathogenic. Select a step to read what it means.
Likely pathogenic.A likely pathogenic classification under the recorded framework.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.MED12 encodes a component of the Mediator protein complex, which helps control the initiation of gene transcription and activates CDK8 kinase. Inherited loss of MED12 function is associated with X-linked developmental disorders, including FG syndrome, Lujan-Fryns syndrome, and Ohdo syndrome. MED12 generally acts as a tumor suppressor, and its disruption has been linked to uterine leiomyomas and several benign breast tumors, as well as altered growth and survival of cancer cells.
The recorded framework is Generic ACMG/AMP 2015 with ClinGen SVI recommendations. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
Met, strong: exact p.Gly44Asp showed reproducibly reduced Cyclin C/CDK8/CDK19 binding (AP-MS n=3) and independent cellular signaling abnormalities versus wild type.
Met: codon 44 contains 74% of reported MED12 mutations and is a statistically significant hotspot, with the variant absent from gnomAD v2.1 and v4.1.
Met at supporting strength: the variant is absent from gnomAD v2.1 and v4.1, consistent with frequency <=0.0001.
No benign criterion marked as applied in the recorded assessment.
Likely Pathogenic: PS3 strong plus PM1 moderate and PM2 supporting satisfy the generic ACMG/AMP 2015 combination rule.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1 allele counts were not recorded for this variant.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
Recorded SpliceAI maximum delta score: 0.037. Refer to the recorded PP3/BP4 rationale for interpretation.
1 other. ClinVar API review status: no assertion criteria provided.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Oncogenic.
This variant has previously been reported in somatic cancers (COSMIC; COSV61329353, n = 856 times).
This variant lies in a statistically significant hotspot.
ACMG/AMP criteria under Generic ACMG/AMP 2015 with ClinGen SVI recommendations, with the data and sources behind each one.
28 criteria with recorded statuses: 3 met · 9 not met · 12 not assessed · 4 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
PM1 is met from the recurrent codon-44 hotspot evidence and absence of the variant from gnomAD; PS1 and PM5 are not established because the available reports do not provide qualifying pathogenic comparator variants.
PP2 and BP1 remain not assessed because the supplied evidence does not establish their required gene-level missense or truncating-variant premises.
PS2, PM6, PP1, and BS4 are not assessed because the available evidence contains no germline proband-parent testing, family pedigree, informative meioses, or affected-relative segregation data.
The exact MED12 c.131G>A / p.Gly44Asp variant has direct biochemical and cellular functional studies, including reproducible protein-complex disruption and independent abnormal signaling phenotypes.
The combined evidence supports PS3 at strong strength under the generic ACMG/AMP functional-study definition.
The same evidence is damaging rather than benign, so BS3 is not met; no neutral functional result was identified.
No VCEP covers MED12 in this case; the requested criteria were evaluated under generic ACMG/AMP rules.
The literature packet's PS4-indexed paper, PMID:26822237, was checked against its extracted full text and does not mention the exact queried variant.
No criterion outside PS4, PP4, PP5, BP5, and BP6 was adjudicated.
Generic ACMG/AMP rules govern because no VCEP covers MED12.
The variant is missense, so PP3 and BP4 are restricted to the REVEL path; REVEL is unavailable and neither SpliceAI nor uncalibrated BayesDel can substitute.
Population evidence supports PM2 at supporting strength; BA1 and BS1 are not met, and BS2 is not assessable because no healthy adult observation is documented.
No criteria match.
PS3 is met at strong strength. Turunen et al. directly tested the exact MED12 p.Gly44Asp substitution corresponding to NM_005120.3:c.131G>A in engineered human 293T-REx cells and found a specific, reproducible reduction in binding of Cyclin C, CDK8, and CDK19 to mutant versus wild-type MED12 (AP-MS, n=3), with loss of kinase-module association while core Mediator association was retained. Immunoblotting, immunoprecipitation-Western analysis, recombinant kinase-module reconstitution, and in-vitro kinase assays provided orthogonal evidence of impaired MED12-Cyclin C-CDK8/19 interaction and reduced associated kinase activity. Independently, El Andaloussi et al. studied the exact c.131G>A construct in immortalized human uterine myometrial smooth-muscle cells and observed increased Wnt4/beta-catenin, S-phase and cyclin D1, increased total and phosphorylated mTOR, and altered autophagy markers compared with MED12 wild type. These variant-specific, controlled, mechanistically concordant functional results support a damaging effect on MED12. The studies are not validated clinical-diagnostic assays and use engineered or overexpression systems, but the direct biochemical assay with reproducibility and the independent cellular phenotype support the full PS3 code under the generic ACMG/AMP definition.
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
MED12 p.Gly44Asp is at codon 44, a recurrent MED12 exon 2 hotspot: 52 of 70 MED12 mutations in the breast phyllodes cohort involved codon 44 (74%), and the Cancer Hotspots result identifies MED12 G44 as a statistically significant hotspot. The exact variant is absent from gnomAD v2.1 and v4.1, providing no observed population benign variation for this variant. The Cancer Hotspots extraction is flagged as partially parsed, so the hotspot record should receive human confirmation.
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
PM2 is met at supporting strength. NM_005120.3:c.131G>A (MED12 p.Gly44Asp) was absent from gnomAD v2.1 and gnomAD v4.1, and was also absent from the available non-cancer cohort checks. The available datasets therefore provide an observed frequency of zero, which is below the generic PM2 supporting threshold of <=0.0001; no ancestry-specific or cohort-specific frequency artifact is present in the reported evidence.
Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
PS4 is not met. The PS4-indexed paper, PMID:26822237, was verified in its extracted full-text finding and does not mention MED12 c.131G>A or p.G44D; it reports MED12 mutations in 3 of 121 pediatric solid-tumor WES reports but provides neither variant-specific affected-case counts nor unaffected/population controls. PMID:26018969 reports the exact somatic variant in 18 of 112 breast phyllodes tumors (16.1%), and PMID:28771672 reports it in 3 CLL patients, but neither study supplies a matched control comparison for this variant or a case-control OR and 95% CI. The governing ACMG/AMP definition requires a significantly increased prevalence in affected individuals compared with controls; therefore no qualifying case-control evidence is present. No numeric comparison was performed because the required case and control counts for the queried variant were unavailable.
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0.
Scope was settled first: NM_005120.3:c.131G>A is a missense variant, p.(Gly44Asp), so the generic PP3/BP4 rule permits the REVEL path only. No REVEL score is available for this variant. The available BayesDel score cannot be used because no generic ACMG-strength calibration is established, and the SpliceAI result cannot be substituted for the missense path. Therefore PP3 is not met.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only. ... An indeterminate result on the applicable path means PP3/BP4 are simply not met.
PP5 is not met. ClinVar variation 92220 records the queried MED12 c.131G>A (p.Gly44Asp) variant as 'other' with no assertion criteria provided and no expert-panel submission; the available submissions are ordinary laboratory or non-classifying somatic records, not an exact-variant ClinVar expert-panel pathogenic or likely pathogenic classification.
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
BA1 is not met. NM_005120.3:c.131G>A (MED12 p.Gly44Asp) was absent from gnomAD v2.1 and gnomAD v4.1, including the available non-cancer cohort checks, so the filtering allele frequency is below the generic stand-alone benign threshold of >=0.05. No population frequency, ancestry-specific elevation, or high-frequency threshold artifact supports BA1.
Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
BS1 is not met. The variant was absent from gnomAD v2.1 and gnomAD v4.1, as well as the available non-cancer cohort checks, so there is no observed allele frequency greater than expected for the disorder and no frequency basis for the generic >=0.01 default. A maximum-credible-frequency calculation is unnecessary because the observed frequency is zero in the available reference datasets.
Allele frequency is greater than expected for the disorder.
BS3 is not met. The exact variant has variant-specific functional evidence showing impaired MED12 protein-complex interaction, reduced associated CDK8/19 kinase activity, and abnormal cellular signaling relative to wild-type MED12, rather than evidence of no damaging effect on protein function or splicing. No well-established assay in the reviewed sources demonstrated a normal functional result for NM_005120.3:c.131G>A / p.Gly44Asp.
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
Scope was settled first: NM_005120.3:c.131G>A is a missense variant, p.(Gly44Asp), so the generic PP3/BP4 rule permits the REVEL path only. No REVEL score is available for this variant, making the applicable path indeterminate. The available SpliceAI result cannot be substituted for the missense path, and BayesDel has no generic ACMG-strength calibration. Therefore BP4 is not met.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) ... Missense variant -> REVEL only. ... An indeterminate result on the applicable path means PP3/BP4 are simply not met.
BP5 is not met. The evidence reports the queried variant in somatic tumor cohorts and experimental tumor-cell models, but does not document a patient with a defined disease who has an established alternate molecular basis for that disease. Somatic occurrence or a tumor-study context alone does not satisfy BP5.
Variant found in a case with an alternate molecular basis for disease.
BP6 is not met. ClinVar variation 92220 does not contain an exact-variant expert-panel benign or likely benign classification; its classification is 'other' with no assertion criteria provided and no expert-panel submission. Ordinary laboratory submissions, aggregate labels, and non-expert assertions cannot trigger BP6.
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
The queried variant is MED12 c.131G>A, p.Gly44Asp, and the literature reports this same amino-acid change. However, the supplied ClinVar record is classified as "other" with no assertion criteria, and the papers do not establish p.Gly44Asp as a pathogenic variant. Therefore, the required previously established pathogenic comparator for PS1 is not available.
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.
No clinical proband report with confirmed maternity and paternity, de novo status, disease phenotype, and absence of family history was identified. The available exact-variant literature concerns somatic tumor cohorts or engineered cell models and does not establish a germline de novo event.
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
PM3 cannot be assessed because the available evidence does not document an affected proband with a second pathogenic MED12 variant, parental or offspring testing, or confirmed trans phase. The available exact-variant publications describe somatic tumor observations or engineered-cell experiments and do not establish the recessive inheritance context or biallelic germline state required for this criterion.
For recessive disorders, detected in trans with a pathogenic variant
The supplied literature reports the queried p.Gly44Asp change repeatedly, but no different missense substitution at residue 44 is identified as pathogenic. The recurrence of the same p.Gly44Asp change cannot satisfy PM5, and the available evidence does not establish a qualifying alternate missense comparator.
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.
No clinical proband report was identified that supports an assumed de novo occurrence of the variant. The available exact-variant literature does not provide parental testing or a germline family-based observation from which de novo status could be assumed.
Assumed de novo, but without confirmation of paternity and maternity.
No affected family members, informative meioses, or variant-positive and variant-negative relatives with phenotype data were reported. The available exact-variant studies are somatic tumor cohorts or cell-based experiments and cannot establish cosegregation in a disease family.
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.
The supplied evidence documents recurrent MED12 missense mutations in somatic tumours and functional effects of p.Gly44Asp, but it does not provide a gene-wide measure showing a low rate of benign missense variation together with evidence that missense variants are a common disease mechanism in the relevant disease context. Both required PP2 components therefore remain unestablished.
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
PP4 was not assessed because the supplied evidence contains no patient-level phenotype or family-history description for the queried variant and no defined single-gene disease phenotype against which specificity can be judged.
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
BS2 cannot be assessed from the available evidence. The case contains no documented observation of this variant in a healthy adult individual, and the available gnomAD records report absence rather than healthy-carrier or healthy-hemizygote observations. The inheritance model, expected penetrance, and age-of-onset requirements for a specific MED12 disorder are also not established in the case evidence.
Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.
No affected family members were reported who lacked the variant, and no pedigree or family testing data were identified. Therefore, lack of segregation cannot be evaluated; the available somatic and experimental studies do not provide evidence for BS4.
Lack of segregation in affected members of a family.
The supplied materials do not establish that MED12 disease is caused primarily by truncating variants. They contain reports of MED12 missense mutations and general disease-mechanism context, but no sufficiently characterized variant spectrum demonstrating the BP1 gene-level premise.
Missense variant in a gene for which primarily truncating variants are known to cause disease.
BP2 cannot be assessed because the available evidence does not document this variant with a pathogenic variant in trans in a fully penetrant dominant MED12 disorder or with a pathogenic variant in cis in any inheritance context. The exact-variant publications report somatic tumor findings or cell experiments without germline phase, cis/trans status, or a qualifying dominant proband observation.
Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.
PVS1 (ClinGen SVI PVS1 recommendations, PMC6185798, pvs1_generic_framework) applies only to null variant classes — nonsense, frameshift, canonical ±1/2 splice-consensus, translation-initiation-codon loss, and stop-loss variants — each expected to trigger nonsense-mediated decay or otherwise abolish normal protein function. NM_005120.3:c.131G>A in MED12 is a missense substitution predicted to produce NP_005111.2:p.(Gly44Asp). As a result, no null-variant mechanism (nonsense-mediated decay, truncation, or canonical splice disruption) is triggered by this variant class, so PVS1's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PVS1 for MED12, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_null_variant_class
PM4 (Richards et al. 2015, PMID:25741868) applies to protein length changes: in-frame insertions/deletions in a non-repetitive region, or stop-loss variants that extend the protein past the reference stop codon. NM_005120.3:c.131G>A in MED12 is a missense substitution predicted to produce NP_005111.2:p.(Gly44Asp). As a result, no change in protein length occurs, so there is nothing for this criterion to evaluate, so PM4's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PM4 for MED12, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_stop_loss_or_nonrepeat_indel
BP3 (Richards et al. 2015, PMID:25741868) applies to in-frame insertions/deletions located in a repetitive region without a known function. NM_005120.3:c.131G>A in MED12 is a missense substitution predicted to produce NP_005111.2:p.(Gly44Asp). As a result, the variant does not alter protein length within a repeat region, so there is nothing for this criterion to evaluate, so BP3's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP3 for MED12, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_repeat_region_indel
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_005120.3:c.131G>A in MED12 is a missense substitution predicted to produce NP_005111.2:p.(Gly44Asp). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for MED12, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
Every interpreted variant in MED12, mapped onto the exon structure of NM_005120.3. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
Scope was settled first: NM_005120.3:c.131G>A is a missense variant, p.(Gly44Asp), so the generic PP3/BP4 rule permits the REVEL path only. No REVEL score is available for this variant. The available BayesDel score cannot be used because no generic ACMG-strength calibration is established, and the SpliceAI result cannot be substituted for the missense path. Therefore PP3 is not met.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only. ... An indeterminate result on the applicable path means PP3/BP4 are simply not met.
Scope was settled first: NM_005120.3:c.131G>A is a missense variant, p.(Gly44Asp), so the generic PP3/BP4 rule permits the REVEL path only. No REVEL score is available for this variant, making the applicable path indeterminate. The available SpliceAI result cannot be substituted for the missense path, and BayesDel has no generic ACMG-strength calibration. Therefore BP4 is not met.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) ... Missense variant -> REVEL only. ... An indeterminate result on the applicable path means PP3/BP4 are simply not met.
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_005120.3:c.131G>A in MED12 is a missense substitution predicted to produce NP_005111.2:p.(Gly44Asp). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for MED12, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04). BayesDel score = 0.551967.
6 paper records listed. 3 cited in the classification.
Affinity-purification mass spectrometry (AP-MS) revealed a specific and reproducible (n = 3) reduction in the binding of Cyclin C, CDK8 and CDK19 to mutant versus wild-type MED12.
Location Results and Discussion, ‘Uterine leiomyoma-linked mutations in MED12 disrupt its association with CycC-CDK8/19,’ first paragraph; Fig. 1B-E
Context Engineered tetracycline-inducible Flp-In 293T-REx cells expressing Twin-Strep-tagged wild-type or G44D MED12; AP-MS, immunoblotting, immunoprecipitation-Western analysis, recombinant baculovirus-expressed kinase-module reconstitution, and in-vitro kinase assays.
c.131G>A p.G44D 18 16.1
Location Table 2, “High frequency of MED12 exon 2 mutations in phyllodes tumours of breast”; Discussion paragraph beginning “In this series of breast phyllodes tumours”
Context Cohort of 112 breast phyllodes tumours; ultra-deep targeted amplicon sequencing of MED12 exon 2 using formalin-fixed, paraffin-embedded tumour DNA and Illumina MiSeq sequencing.
Using an immortalized human uterine myometrial smooth muscle cell line (UtSM), we constitutively overexpressed either MED12-Wild Type or the most common MED12 somatic mutation (c.131G>A).
Location Abstract; Materials and Methods, “Generation of Stable MED12-WT and MED12-Mut UtSM Cell Lines”; Results, Figs. 2–5; Conclusion
Context Ectopic expression of MED12-WT or c.131G>A in stable populations and clones of an immortalized uterine myometrial smooth-muscle cell line, with biochemical, cell-cycle, gene-expression, and ultrastructural assays.
5 Male 2 c.G131A p.G44D 1·00 43 Female 2 c.G131A p.G44D 0·55 45 Female 2 c.G131A p.G44D N.A.
Results, Table I (Somatic mutations affecting MED12 identified in 188 CLL patients)
BCOR, DDX3X, and MED12 (3 of 121 each, 2.5%)
Results, Tumor WES, paragraph 2
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The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
This variant has been reported in ClinVar as other (1 clinical laboratory). (ClinVarID = 92220)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04). BayesDel score = 0.551967.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Oncogenic.
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV61329353, n = 856 times).
This variant lies in a statistically significant hotspot.