NM_005089.3:c.398_399del

ZRSR2 · NP_005080.1:p.(Glu133GlyfsTer11) · NM_005089.3

GRCh37: chrX:15822316 AAG>A · GRCh38: chrX:15804193 AAG>A

Gene: ZRSR2 Transcript: NM_005089.3

Final call

Likely Pathogenic

PVS1 very strong PM2 moderate

Variant details

Gene

ZRSR2

Transcript

NM_005089.3

Protein

NP_005080.1:p.(Glu133GlyfsTer11)

gnomAD AF

ClinVar

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_005089.3:c.398_399del is a frameshift variant in exon 5 of ZRSR2 predicted to cause premature termination at codon 143 (p.Glu133GlyfsTer11), resulting in loss of approximately 70% of the protein including functionally critical zinc finger and RS-rich domains.

ZRSR2 loss-of-function is an established germline disease mechanism: germline ZRSR2 mutations cause oral-facial-digital syndrome (PMID:38158857) and have been reported in constitutional aplastic anemia (PMID:35371815). ZRSR2 is a core component of the minor (U12) spliceosome, and its depletion causes widespread U12-type intron retention (PMID:25586593).

Under the ClinGen SVI PVS1 decision framework (PMC6185798), a frameshift variant in a gene with an established LOF disease mechanism is classified as PVS1 at very_strong strength. NMD is predicted as the premature termination codon occurs in exon 5 of 11.

The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, supporting PM2 at moderate strength (allele frequency <0.1% per generic ACMG thresholds).

The variant has been observed once in a somatic cancer sample (COSMIC COSV57067023), consistent with its predicted loss-of-function effect, though this somatic observation is not directly applied to germline ACMG criteria.

No variant-specific functional studies, de novo observations, segregation data, or ClinVar classifications were identified for this variant.

Combined evidence: 1 Very_Strong (PVS1) + 1 Moderate (PM2) meets the generic ACMG/AMP Likely Pathogenic classification threshold (1 Very_Strong + 1 Moderate).

Final determination: Generic ACMG/AMP 2015 fallback rules support a Likely Pathogenic classification based on the observed combination of pathogenic criteria.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Met	NM_005089.3:c.398_399del is a frameshift variant in exon 5 of 11, predicted to cause premature termination at codon 143 (p.Glu133GlyfsTer11), removing 340 of 483 amino acids including the zinc finger and RS-rich domains. NMD is predicted as the premature termination codon occurs more than 55 nucleotides upstream of the last exon-exon junction. ZRSR2 loss-of-function is an established germline disease mechanism supported by literature describing germline ZRSR2 mutations in oral-facial-digital syndrome and aplastic anemia. Under the ClinGen SVI PVS1 decision framework (PMC6185798), frameshift variants meeting the gene-level LOF gate are classified as PVS1 at very_strong strength.	pvs1_generic_framework pvs1_gene_context pvs1_variant_assessment PMID:25586593
PS1	N/A	NM_005089.3:c.398_399del is a 2-nucleotide deletion causing a frameshift; PS1 applies only to single-nucleotide variants where a different nucleotide change at the same position has been previously established as pathogenic.
PS2	Not met	No de novo observation data is available for NM_005089.3:c.398_399del. No proband narratives or confirmed parental testing results were provided.
PS3	Not met	No variant-specific functional data exists for NM_005089.3:c.398_399del. PMID:25586593 provides gene-level functional evidence that ZRSR2 loss-of-function disrupts U12-dependent splicing, but does not test or report this specific variant. The paper studied eight MDS patients with ZRSR2 nonsense/frameshift mutations via RNA-Seq and performed shRNA knockdown experiments; none of the specific mutations are listed as c.398_399del nor is codon 133 mentioned. This paper represents domain-level/gene-level mechanistic evidence appropriate for PVS1 and PM1 contexts, not PS3 variant-specific functional data.	PMID:25586593
PS4	Not met	No case-control or statistical enrichment data is available for NM_005089.3:c.398_399del. The variant has been observed once in COSMIC (COSV57067023, somatic), but this does not constitute germline case-control evidence for PS4.
PS5	Not met	No previously established pathogenic variant has been reported that causes the same protein change (p.Glu133GlyfsTer11) at this position. ClinVar contains no entries for NM_005089.3:c.398_399del or variants at the same codon.	clinvar
PM1	Not met	Position p.Glu133 is not located within a statistically significant mutational hotspot (cancerhotspots.org: no significant residue-level enrichment). While the frameshift truncates most of the ZRSR2 protein including functionally characterized C-terminal domains (zinc finger at ~280-310, RS-rich domain), PM1 is typically assigned to missense variants within well-defined functional domains. The truncation evidence is more appropriately captured under PVS1. No specific functional domain boundary has been characterized at or immediately surrounding residue 133.	PMID:25586593
PM2	Met	NM_005089.3:c.398_399del is absent from all population databases queried, including gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes). For a rare disease-associated gene on the X chromosome, complete absence from large population cohorts (<0.1% under non-VCEP generic ACMG) supports a pathogenic interpretation.	gnomad_v2 gnomad_v4 gnomad_canada
PM3	N/A	Skipped per adjudication instruction (trivially not_applicable).
PM4	N/A	PM4 applies to in-frame deletions/insertions in non-repeat regions or stop-loss variants. NM_005089.3:c.398_399del is a 2-nucleotide frameshift deletion causing a premature stop codon (p.Glu133GlyfsTer11), which is an out-of-frame change assessed under PVS1, not PM4.
PM5	N/A	PM5 requires a different missense variant at the same residue that has been classified as pathogenic. NM_005089.3:c.398_399del is a frameshift deletion; no same-residue missense comparator semantics apply. The automated PM5 candidate harvesting system confirmed this variant is not eligible for classic PM5 analysis.	pm5_candidates
PM6	Not met	No de novo observation data is available for NM_005089.3:c.398_399del. No confirmed maternity/paternity testing results were reported.
PP1	Not met	No segregation data is available for NM_005089.3:c.398_399del. No affected family members or co-segregation analyses were reported.
PP2	N/A	PP2 applies specifically to missense variants in genes where missense variants are a common disease mechanism and benign missense variation is rare. NM_005089.3:c.398_399del is a frameshift variant; PP2 does not apply to truncating variants.
PP3	Not met	SpliceAI predicts no significant splice impact (max delta score = 0.02). REVEL and BayesDel scores are not applicable (variant is not an SNV). No HCI prior score is available. For a frameshift variant, the deleterious effect is inherent in the variant type and captured under PVS1; in silico evidence adds no additional support.	spliceai
PP4	Not met	No patient-specific phenotype or clinical information was provided for this case. PP4 requires that the patient's phenotype or family history is highly specific for the gene/disease.
PP5	Not met	NM_005089.3:c.398_399del is absent from ClinVar. No reputable source has reported this variant as pathogenic. PP5 requires a ClinVar classification from a reputable source (ideally expert panel, 3-star or above).	clinvar
BA1	Not met	NM_005089.3:c.398_399del is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. The allele frequency is 0%, well below the BA1 threshold of >1%.	gnomad_v2 gnomad_v4
BS1	Not met	NM_005089.3:c.398_399del is absent from all population databases. The allele frequency is 0%, well below the BS1 threshold of >0.3% for non-VCEP generic ACMG.	gnomad_v2 gnomad_v4
BS2	Not met	NM_005089.3:c.398_399del has not been observed in healthy adult individuals. BS2 requires observation of the variant in a healthy control inconsistent with disease penetrance — no such observation exists.
BS3	Not met	The only functional study available (PMID:25586593) demonstrates that ZRSR2 loss-of-function disrupts U12-dependent splicing, which supports a deleterious effect consistent with pathogenicity. There is no evidence from well-established functional studies showing a normal or benign effect of this variant on protein function or splicing.	PMID:25586593
BS4	Not met	No segregation data is available for NM_005089.3:c.398_399del. BS4 requires lack of segregation in affected family members — no family segregation analysis was performed.
BP1	N/A	BP1 applies to missense variants in genes where primarily truncating variants are the known disease mechanism. NM_005089.3:c.398_399del is itself a truncating (frameshift) variant, so BP1 does not apply.
BP2	Not met	No observation of NM_005089.3:c.398_399del in trans with a known pathogenic variant in ZRSR2 or in cis with a pathogenic variant. BP2 requires such an observation to support a benign interpretation.
BP3	N/A	BP3 applies to in-frame deletions/insertions in repetitive regions without known function. NM_005089.3:c.398_399del is a 2-nucleotide frameshift deletion, not an in-frame change in a repetitive region.
BP4	Not met	SpliceAI predicts no significant splice impact (max delta = 0.02), but this computational evidence does not suggest a benign effect for a frameshift variant. The variant's truncating nature is inherently damaging; BP4 is typically reserved for missense variants where multiple lines of computational evidence suggest no impact.	spliceai
BP5	Not met	No report of NM_005089.3:c.398_399del being found in a case with an alternate molecular basis for disease. BP5 requires an alternate pathogenic variant identified that explains the phenotype.
BP6	Not met	NM_005089.3:c.398_399del is absent from ClinVar. No reputable source has reported this variant as benign or likely benign.	clinvar
BP7	N/A	BP7 applies to synonymous variants with no predicted splice impact and low nucleotide conservation. NM_005089.3:c.398_399del is a frameshift deletion, not a synonymous variant.

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