Is SRCAP p.Gly2276Val (c.6827G>T) pathogenic?

SRCAP p.Gly2276Val (c.6827G>T) is classified Likely benign in SRCAP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-25). AlphaMissense: likely benign (0.094); Ultra-rare (popmax 0.0356%, eas); Associated with Inborn genetic diseases.

What condition is associated with SRCAP p.Gly2276Val (c.6827G>T)?

SRCAP p.Gly2276Val (c.6827G>T) is associated with Inborn genetic diseases (ClinVar).

How common is SRCAP p.Gly2276Val (c.6827G>T) in the general population?

SRCAP p.Gly2276Val (c.6827G>T) is ultra-rare (popmax 0.0356%, eas) (gnomAD).

What do computational predictors say about SRCAP p.Gly2276Val (c.6827G>T)?

AlphaMissense predicts likely benign (score 0.094) — an in-silico prediction, not a clinical call.

SRCAP p.Gly2276Val

c.6827G>T · rs141357480 · VCV3169844

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.094 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0356%, eas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.094	likely benign
REVEL	0.32	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.5	GERP 1.4, phastCons 1
Regional constraint	o/e 0.60	unconstrained · MANE · 918 bp · p 1.2e-06 · regional, not allelic
Overall
CADD	22.3	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

Grpmax group 0.0356% East Asian · 16/44,896 alleles

Filtering AF 0.0223% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0182%

Overall 0.000991% 16/1,614,034 alleles · ultra-rare exomes 14/1,461,882 · genomes 2/152,152 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: SRCAP
Protein: p.Gly2276Val
Coding: c.6827G>T
MANE Select: NM_006662
dbSNP: rs141357480
Type: single nucleotide variant
Location: chr16:30736297 (GRCh38)
Gene constraint: LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 2276: the 'disordered' region; a UniProt-annotated variant site (in dehmba)

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SRCAP p.Gln2407Ter Pathogenic ★★ same condition
SRCAP p.Ala1152Val Uncertain significance ★★ ⚠ same condition
SRCAP p.Ala1161Thr Uncertain significance ★★ ⚠ same condition
SRCAP p.Ala1570Thr Uncertain significance ★★ ⚠ same condition
SRCAP p.Ala1584Gly Uncertain significance ★★ same condition
SRCAP p.Ala1985Thr Uncertain significance ★★ same condition
SRCAP p.Ala2699Val Uncertain significance ★★ ⚠ same condition
SRCAP p.Ala2945Val 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-gly2276val (accessed [today's date]).

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