Is SGMS2 p.Ser310Phe (c.929C>T) pathogenic?

SGMS2 p.Ser310Phe (c.929C>T) is classified Uncertain significance in SGMS2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-29). AlphaMissense: likely pathogenic (0.7026); Absent from gnomAD v4.1.

How common is SGMS2 p.Ser310Phe (c.929C>T) in the general population?

SGMS2 p.Ser310Phe (c.929C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SGMS2 p.Ser310Phe (c.929C>T)?

AlphaMissense predicts likely pathogenic (score 0.7026) — an in-silico prediction, not a clinical call.

SGMS2 p.Ser310Phe

c.929C>T · rs2476844205 · VCV2826341

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7026 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.7026	likely pathogenic
REVEL	0.294	indeterminate
SaProt	LLR -8.11	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 7.7	GERP 2.2, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 15 kb · p 0.0049 · regional, not allelic
Overall
CADD	24.7	PHRED · no single calibrated threshold — expert panels disagree

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: SGMS2
Protein: p.Ser310Phe
Coding: c.929C>T
dbSNP: rs2476844205
Type: single nucleotide variant
Location: chr4:107910384 (GRCh38)

Full SGMS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/sgms2-p-ser310phe (accessed [today's date]).

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