The RAC1 NM_018890.4:c.85C>T (NP_061485.1:p.(Pro29Ser)) missense variant has previously been reported in somatic cancers (COSMIC; COSV61821563, n = 178 times), and lies in a statistically significant hotspot (cancerhotspots.org). Experimental evidence: Independent biochemical, cellular, and mouse-xenograft assays consistently demonstrated RAC1 P29S gain of function versus wild type. Based on available guidelines, this variant is considered to be Pathogenic.
Five-step scale from benign to pathogenic. This variant is pathogenic. Select a step to read what it means.
Pathogenic.A 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.RAC1 encodes a small GTPase that helps regulate cell growth, cell shape and movement, adhesion, differentiation, and signaling pathways involved in inflammation and the cell cycle. Changes that increase RAC1 activity are associated with cancer development and progression, especially melanoma, and can contribute to metastasis and resistance to treatment. An alternatively spliced, continuously active form called RAC1B has also been identified in colon and lung cancer.
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: independent biochemical, cellular, and mouse-xenograft assays consistently demonstrated RAC1 P29S gain of function versus wild type.
Met: melanoma case-control comparisons gave corrected ORs 275.18 and 539.02, both >5.0 with 95% confidence intervals excluding 1.0.
Met at moderate strength: P29S is a statistically significant recurrent hotspot, reported in 4%–9% of melanomas and absent from gnomAD v2.1 and v4.1.
Met at supporting strength: the variant was absent from gnomAD v2.1 and v4.1, below the PM2 threshold of <=0.0001.
Met: all three RAC1 P29S cases in a 45-patient cohort also had BRAF V600-mutant melanoma, providing an alternate molecular basis.
Pathogenic: PS3 and PS4 at strong strength satisfy the generic ACMG two-Strong rule, with PM1 moderate and PM2 supporting additional pathogenic evidence.
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 REVEL score: 0.585. Refer to the recorded PP3/BP4 rationale for interpretation.
A ClinVar laboratory submission summary was not recorded.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Oncogenic.
This variant has previously been reported in somatic cancers (COSMIC; COSV61821563, n = 178 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: 5 met · 4 not met · 15 not assessed · 4 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Generic ACMG/AMP rules govern because no RAC1 VCEP or gene-specific specification is present.
PM1 is met at moderate strength from the statistically significant recurrent RAC1 P29 hotspot and supporting absence of observed benign or population variation.
PS1, PM5, PP2, and BP1 remain not assessed because their required comparator or gene-level evidence was not established.
PS2, PM6, PP1, and BS4 are not assessed because the available evidence contains no germline proband-parent testing, pedigree, affected-relative genotypes, or familial segregation/non-segregation data.
Somatic melanoma reports and functional studies do not substitute for the proband, parental, phenotype, meiosis, or family-segregation evidence required by these criteria.
The functional evidence supports PS3 at strong strength because independent biochemical, cellular, and in-vivo assays directly tested RAC1 P29S and consistently demonstrated gain of function.
BS3 was not assessed because no validated assay demonstrated no damaging effect on RAC1 P29S protein function or splicing.
PS4 is supported by strong enrichment of RAC1 P29S in melanoma cases versus germline/population controls, with corrected ORs far above the >5.0 threshold and confidence intervals excluding 1.0.
BP5 is supported by co-occurrence of RAC1 P29S with BRAF V600-mutant melanoma, an alternate molecular basis, in the reported clinical cohort.
PP4, PP5, and BP6 cannot be assessed from the available patient phenotype and failed ClinVar verification.
Generic ACMG/AMP rules govern because no RAC1 VCEP is present.
This is a missense variant, so PP3 and BP4 are adjudicated exclusively from REVEL; the REVEL score of 0.585 falls between the supplied PP3 and BP4 supporting cutoffs.
No criteria match.
PS3 is met at strong strength for RAC1 NM_018890.4:c.85C>T (p.Pro29Ser). Multiple independent variant-specific functional studies demonstrate a damaging gain-of-function effect: recombinant-protein assays showed significantly increased GDP-to-GTP exchange and increased PAK1/MLK3 effector binding relative to wild type; cellular assays showed activated RAC1 phenotypes including membrane ruffling, increased melanocyte proliferation and migration; and isogenic melanoma models showed increased RAF-inhibitor resistance, reduced apoptosis, sustained MAPK signaling, and reduced RAF-inhibitor effect on tumor growth in mouse xenografts. The assays directly tested the variant, included wild-type comparisons, covered biochemical, cellular, and in-vivo endpoints, and were concordant. These findings satisfy the ACMG/AMP definition of well-established in-vitro and in-vivo functional studies supportive of a damaging effect. No BS3 evidence was identified that would counterbalance the concordant damaging functional results.
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
PS4 is met under the generic ACMG/AMP definition. PMID:22842228 reports RAC1 c.85C>T/p.Pro29Ser in 7 of 147 melanomas and in 20 of 217 sun-exposed melanomas, while the variant was absent from 2,577 Yale germline exomes and 2,596 individuals from 57 populations. Treating the zero-control cells with a 0.5 continuity correction, the 7/147 comparison gives OR=275.18 with 95% CI 15.64-4842.63, and the 20/217 comparison gives OR=539.02 with 95% CI 32.48-8945.80. The required comparison is OR > 5.0: 275.18 > 5.0? yes; both confidence intervals exclude 1.0. PMID:25465943 independently reports the variant in approximately 4-7% of sun-exposed melanomas and absence from benign nevi. These are somatic melanoma observations compared with germline/population controls, so human review is warranted for application to the present interpretation.
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.
RAC1 p.Pro29Ser lies at the P29 recurrent melanoma hotspot. Cancer Hotspots reports that the variant lies in a statistically significant hotspot, and multiple full-text studies describe c.85C>T/p.Pro29Ser as a recurrent protein-coding hotspot mutation occurring in approximately 4% to 9% of melanomas. The variant was absent from gnomAD v2.1 and v4.1, and the reviewed literature reports absence from benign nevi or germline population datasets, supporting the absence of observed benign variation relevant to this hotspot.
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_018890.4:c.85C>T (RAC1 p.Pro29Ser) was absent from gnomAD v2.1 and gnomAD v4.1, and the available gnomAD v2.1 non-cancer and v3.1 non-cancer searches were also absent. This is below the generic ClinGen SVI supporting threshold of <=0.0001; no cancer-cohort or exome-only override was required because no governing VCEP specification exists and all relevant queried datasets were absent.
Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
BP5 is met at supporting strength. PMID:25056119 describes a clinical cohort of 45 patients with BRAF V600-mutant metastatic melanoma and reports that the three patients with RAC1 P29S all belonged to the early-resistance subgroup. BRAF V600 is an alternate molecular basis present in the same melanoma cases, satisfying the generic BP5 wording, although the evidence is from somatic melanoma rather than a germline disease workup.
Variant found in a case with an alternate molecular basis for disease.
The variant is a missense substitution, so the governing generic rule selects the REVEL path only; SpliceAI and BayesDel are not counted for PP3. The REVEL score is 0.585, below the generic supporting PP3 threshold of >= 0.644 calibrated by Pejaver et al. 2022 (PMID:36413997), so PP3 is not met.
Missense variant -> REVEL only. ... PP3 (supporting): >= 0.644 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
BA1 is not met. NM_018890.4:c.85C>T (RAC1 p.Pro29Ser) was absent from gnomAD v2.1 and gnomAD v4.1, and also absent from the available gnomAD v2.1 non-cancer and v3.1 non-cancer searches. Therefore no filtering allele frequency or grpmax FAF is available, and the generic stand-alone threshold of >=0.05 is not reached. No popmax point estimate was used.
BA1 (stand-alone): >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868)
BS1 is not met. The variant was absent from gnomAD v2.1 and v4.1, with no filtering allele frequency or grpmax FAF available; the non-cancer searches were also absent. Thus the allele frequency is not greater than expected for the disorder and does not reach the generic default of >=0.01. A maximum-credible-allele-frequency calculation is unnecessary because the observed frequency is zero in the available population datasets; no popmax point estimate was used.
Allele frequency is greater than expected for the disorder.
The variant is a missense substitution, so the governing generic rule selects the REVEL path only; the SpliceAI result cannot substitute for a gray-zone REVEL result, and BayesDel has no generic ACMG-strength calibration. The REVEL score is 0.585, above the generic BP4 supporting threshold of <= 0.29 calibrated by Pejaver et al. 2022 (PMID:36413997), so BP4 is not met.
Missense variant -> REVEL only. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
The variant is RAC1 p.Pro29Ser, but the available evidence does not establish a previously established pathogenic variant causing the same amino-acid change through a different nucleotide change. The literature documents this exact variant as a recurrent somatic melanoma hotspot, not as a previously established pathogenic germline comparator, and the ClinVar lookup failed.
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.
The available case evidence does not document a clinically affected proband with RAC1 c.85C>T, confirmed maternity and paternity, or absence of a family history. The literature reviewed concerns recurrent somatic melanoma observations and functional studies, not a germline de novo family investigation, so PS2 cannot be assessed.
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
PM3 cannot be assessed. The generic PM3 definition applies to recessive disorders and requires the tested variant to be detected in trans with a pathogenic variant, with parental or offspring testing to establish phase. The available case evidence contains no affected-proband observations, no parental or offspring genotypes, no pathogenic second allele, and no documented trans phase; it also does not establish a recessive inheritance mode for the RAC1-associated disorder.
For recessive disorders, detected in trans with a pathogenic variant...This requires testing of parents (or offspring) to determine phase.
No different missense substitution at RAC1 residue Pro29 was identified in the supplied evidence as having been determined pathogenic. The available papers describe p.Pro29Ser itself, and the collected PM5 candidate artifact contains no same-residue comparator candidates; the ClinVar lookup also failed.
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.
The available case evidence does not document an assumed de novo occurrence of RAC1 c.85C>T in a clinically affected proband, nor does it provide parental testing results. Somatic melanoma reports cannot establish germline de novo status, so PM6 cannot be assessed.
Assumed de novo, but without confirmation of paternity and maternity.
No affected family members carrying RAC1 c.85C>T, informative meioses, or co-segregation results are documented. The available variant-specific papers report somatic melanoma cohorts and functional experiments rather than familial segregation, so PP1 cannot be assessed.
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.
The supplied evidence does not provide the two gene-level facts required for PP2: a low rate of benign missense variation and missense variants as a common mechanism of disease for RAC1. Somatic hotspot recurrence and functional gain-of-function findings do not establish those generic gene-level PP2 conditions.
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
The supplied case evidence does not provide the patient's phenotype or family history, and the reviewed RAC1 P29S papers describe melanoma cohorts rather than a highly specific phenotype for a single genetic etiology. PP4 therefore cannot be assessed.
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
PP5 cannot be assessed because the ClinVar lookup failed and no exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification is available. The reviewed publications are not sufficient to trigger PP5 under the required exact-variant expert-panel rule.
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
BS2 is not assessed. The available evidence contains no observation of this variant in a healthy adult individual and no genotype-level evidence establishing a healthy heterozygote, homozygote, or hemizygote. Population absence cannot establish BS2, and the required disorder inheritance, expected penetrance, and age-of-onset context for the healthy-adult rule are not documented.
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.
BS3 cannot be assessed because the reviewed variant-specific studies report activating or otherwise damaging RAC1 P29S effects and do not provide well-established evidence showing no damaging effect on protein function or splicing. The absence of a benign functional result is insufficient to apply BS3, and no validated benign assay result or reproducible normal-splicing assay for this variant was identified in the available evidence.
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
No affected family members with documented RAC1 c.85C>T-negative genotypes are identified, and no informative non-segregation analysis is available. Therefore, lack of segregation cannot be established and BS4 cannot be assessed.
Lack of segregation in affected members of a family.
The supplied evidence does not establish that RAC1 disease is caused primarily by truncating variants. The reviewed RAC1 literature concerns recurrent somatic missense p.Pro29Ser and gain-of-function biology, which is insufficient to determine the gene-level truncating-variant pattern required for BP1.
Missense variant in a gene for which primarily truncating variants are known to cause disease.
BP2 cannot be assessed. The available case evidence contains no pathogenic variant reported in cis or in trans with NM_018890.4:c.85C>T, and no phase-testing results. The evidence also does not establish a fully penetrant dominant RAC1 disorder for an applicable trans observation; therefore neither BP2 path can be evaluated.
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.
BP6 cannot be assessed because the ClinVar lookup failed and no exact-variant ClinVar expert-panel Benign or Likely benign classification is available. No reviewed source provides the required reputable benign assertion under the specified generic rule.
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
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_018890.4:c.85C>T in RAC1 is a missense substitution predicted to produce NP_061485.1:p.(Pro29Ser). 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 RAC1, 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_018890.4:c.85C>T in RAC1 is a missense substitution predicted to produce NP_061485.1:p.(Pro29Ser). 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 RAC1, 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_018890.4:c.85C>T in RAC1 is a missense substitution predicted to produce NP_061485.1:p.(Pro29Ser). 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 RAC1, 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_018890.4:c.85C>T in RAC1 is a missense substitution predicted to produce NP_061485.1:p.(Pro29Ser). 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 RAC1, 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 RAC1, mapped onto the exon structure of NM_018890.4. 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.
The variant is a missense substitution, so the governing generic rule selects the REVEL path only; SpliceAI and BayesDel are not counted for PP3. The REVEL score is 0.585, below the generic supporting PP3 threshold of >= 0.644 calibrated by Pejaver et al. 2022 (PMID:36413997), so PP3 is not met.
Missense variant -> REVEL only. ... PP3 (supporting): >= 0.644 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
The variant is a missense substitution, so the governing generic rule selects the REVEL path only; the SpliceAI result cannot substitute for a gray-zone REVEL result, and BayesDel has no generic ACMG-strength calibration. The REVEL score is 0.585, above the generic BP4 supporting threshold of <= 0.29 calibrated by Pejaver et al. 2022 (PMID:36413997), so BP4 is not met.
Missense variant -> REVEL only. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
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_018890.4:c.85C>T in RAC1 is a missense substitution predicted to produce NP_061485.1:p.(Pro29Ser). 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 RAC1, 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 = 0.01). REVEL score = 0.585. BayesDel score = 9.90479e-05.
5 paper records listed. 4 cited in the classification.
The binding assays showed more complex formation of pure RAC1P29S with PAK1-PBD compared to RAC1WT in the presence of GTP or slowly hydrolysable GTPγS.
Location Results, “Recurrent mutations”; “RAC1P29S mutations”; “Analyses of RAC1P29S effector binding activity”
Context Exome sequencing of 147 melanomas; targeted sequencing of 364 melanomas; 76 melanoma cell lines; matched-normal analysis; structural studies; effector-binding and cell-functional assays.
We found that RAC1P29S is a spontaneously activating GTPase with significantly increased inherent GDP→GTP nucleotide exchange compared with that of RAC1WT.
Location Discussion, paragraph 1
Context In vitro recombinant RAC1 nucleotide-exchange, PAK1 pull-down, and GTP-hydrolysis assays; crystal-structure comparison; transient GFP-RAC1 expression in COS-7 cells; stable Flag-RAC1 expression and fluorescence microscopy in NIH 3T3 fibroblasts.
Recently, two large-scale whole exome sequencing (WES) studies have revealed that in addition to recurrent mutations in BRAF and NRAS, the next most frequently observed somatic protein-coding hotspot mutation in melanoma of cutaneous origin is the RAC1 c.85C>T single-nucleotide variant (SNV) encoding the P29S amino acid change found in approximately 4% to 9% of melanomas (10, 11).
Location Introduction; Results sections on RAC1 P29S mutant melanoma cell lines and inhibitor resistance
Context Melanoma cell-line genotyping; RAC1 activation assays; RAF and MEK inhibitor viability and IC50 assays; isogenic models; mouse xenografts; referenced clinical treatment cohort.
Our functional studies showed that unlike the RAS mutations, RAC1P29S maintains its normal GTPase activity but displays an increased inherent GDP→GTP nucleotide exchange, which keeps it mostly in the active form (4).
Location Main text paragraphs describing RAC1P29S occurrence and functional studies
Context Sequencing of more than 600 sun-exposed melanomas; functional studies in normal melanocytes; biochemical effector-binding studies; drug-response analyses in patient-derived melanoma cell lines.
In conclusion, two lines of evidence indicate that the Ah receptor is not involved in induction of choline kinase activity in Hepa lclc7 cells.
Results/Discussion, conclusion paragraph on page 276
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
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.
ClinVar could not be checked: eSearch failed: HTTP 500.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.585. BayesDel score = 9.90479e-05.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Oncogenic.
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV61821563, n = 178 times).
This variant lies in a statistically significant hotspot.