Is CAP2 p.Tyr316Ter (c.948T>G) pathogenic?

CAP2 p.Tyr316Ter (c.948T>G) is classified Pathogenic in CAP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-08-03). Absent from gnomAD v4.1; Associated with cardiomyopathy, dilated, 2I.

What condition is associated with CAP2 p.Tyr316Ter (c.948T>G)?

CAP2 p.Tyr316Ter (c.948T>G) is associated with cardiomyopathy, dilated, 2I (ClinVar).

How common is CAP2 p.Tyr316Ter (c.948T>G) in the general population?

CAP2 p.Tyr316Ter (c.948T>G) is absent from gnomAD v4.1 (gnomAD).

CAP2 p.Tyr316Ter

c.948T>G · rs764955583 · VCV2574650

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

cardiomyopathy, dilated, 2I

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.004	GERP -4
Overall
CADD	35.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CAP2
Protein: p.Tyr316Ter
Coding: c.948T>G
MANE Select: NM_019894 · reported on NM_006366
dbSNP: rs764955583
Type: single nucleotide variant
Location: chr6:17541094 (GRCh38)
Structure: AlphaFold pLDDT 88.01
Residue 316: the peptidase s1 domain

Full CAP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

cardiomyopathy, dilated, 2I — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CAP2 p.Tyr316His Likely benign ★ same residue
CAP2 p.Arg17His Uncertain significance ★★ ⚠ same condition
CAP2 p.Arg13Gln Uncertain significance ★ ⚠ same condition
CAP2 p.Met1Thr Uncertain significance ★ same condition
CAP2 c.636+1G>A Pathogenic same condition
CAP2 p.Ser291fs Likely pathogenic ★ same condition
CAP2 p.Cys430fs Pathogenic same condition
CAP2 p.His203Arg Uncertain significance ★★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cap2-p-tyr316ter (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown