Is SRCAP p.Gly3125Val (c.9374G>T) pathogenic?

SRCAP p.Gly3125Val (c.9374G>T) is classified Uncertain significance in SRCAP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-05). AlphaMissense: likely pathogenic (0.8963); Absent from gnomAD v4.1; Associated with SRCAP-related disorder.

What condition is associated with SRCAP p.Gly3125Val (c.9374G>T)?

SRCAP p.Gly3125Val (c.9374G>T) is associated with SRCAP-related disorder (ClinVar).

How common is SRCAP p.Gly3125Val (c.9374G>T) in the general population?

SRCAP p.Gly3125Val (c.9374G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SRCAP p.Gly3125Val (c.9374G>T)?

AlphaMissense predicts likely pathogenic (score 0.8963) — an in-silico prediction, not a clinical call.

SRCAP p.Gly3125Val

c.9374G>T · rs2543431651 · VCV2634831

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8963 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

SRCAP-related disorder

Computational evidence

Protein change
AlphaMissense	0.8963	likely pathogenic
REVEL	0.502	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 12	GERP 2.5, phastCons 1
Regional constraint	o/e 1.06	unconstrained · MANE · 2,598 bp · p 0.058 · regional, not allelic
Overall
CADD	24.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

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: SRCAP
Protein: p.Gly3125Val
Coding: c.9374G>T
MANE Select: NM_006662
dbSNP: rs2543431651
Type: single nucleotide variant
Location: chr16:30739414 (GRCh38)
Gene constraint: LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 3125: the 'disordered' region; a UniProt-annotated variant site (in dehmba); a UniProt-annotated variant site (in flhs)

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

Disease context

SRCAP-related disorder

Similar variants

SRCAP p.Arg2435Ter Pathogenic/Likely pathogenic ★★ same condition
SRCAP p.Arg2444Ter Pathogenic ★★ same condition
SRCAP p.Arg2748Ter Pathogenic ★★ same condition
SRCAP p.Gln3043His Uncertain significance ★★ ⚠ same condition
SRCAP p.Gln3202His Uncertain significance ★★ same condition
SRCAP p.Leu2652Arg Uncertain significance ★★ same condition
SRCAP p.Pro1728Ala Uncertain significance ★★ ⚠ same condition
SRCAP p.Thr1745Met 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/srcap-p-gly3125val (accessed [today's date]).

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