Is SHOC2 p.Ser31Phe (c.92C>T) pathogenic?

SHOC2 p.Ser31Phe (c.92C>T) is classified Uncertain significance in SHOC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-29). AlphaMissense: likely benign (0.0987); Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with SHOC2 p.Ser31Phe (c.92C>T)?

SHOC2 p.Ser31Phe (c.92C>T) is associated with Cardiovascular phenotype (ClinVar).

How common is SHOC2 p.Ser31Phe (c.92C>T) in the general population?

SHOC2 p.Ser31Phe (c.92C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SHOC2 p.Ser31Phe (c.92C>T)?

AlphaMissense predicts likely benign (score 0.0987) — an in-silico prediction, not a clinical call.

SHOC2 p.Ser31Phe

c.92C>T · rs758965011 · VCV1766489

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0987 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.0987	likely benign
REVEL	0.387	indeterminate
SaProt	LLR -8.73	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.9	GERP 1.7, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 376 bp · p 0.042 · regional, not allelic
Overall
CADD	23.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: SHOC2
Protein: p.Ser31Phe
Coding: c.92C>T
MANE Select: NM_007373
dbSNP: rs758965011
Type: single nucleotide variant
Location: chr10:110964450 (GRCh38)
Gene constraint: LOEUF 0.201 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 88.00 · 13 PDB
Residue 31: the 'disordered' region

Full SHOC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SHOC2 p.Ser31Pro Uncertain significance ★★ ⚠ same residue
SHOC2 p.Ala298Thr Uncertain significance ★★ ⚠ same condition
SHOC2 p.Ala304Thr Uncertain significance ★★ ⚠ same condition
SHOC2 p.Ala580Thr Uncertain significance ★★ ⚠ same condition
SHOC2 p.Arg366Gln Uncertain significance ★★ ⚠ same condition
SHOC2 p.Asn248Thr Uncertain significance ★★ ⚠ same condition
SHOC2 p.Asp210Asn Uncertain significance ★★ ⚠ same condition
SHOC2 p.Asp49Asn Uncertain significance ★★ ⚠ same condition

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/shoc2-p-ser31phe (accessed [today's date]).

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