Is SRCAP p.Arg1897Gln (c.5690G>A) pathogenic?

SRCAP p.Arg1897Gln (c.5690G>A) is classified Likely benign in SRCAP (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-01). AlphaMissense: likely pathogenic (0.6077); Very rare (popmax 0.00267%, afr); Associated with Inborn genetic diseases.

What condition is associated with SRCAP p.Arg1897Gln (c.5690G>A)?

SRCAP p.Arg1897Gln (c.5690G>A) is associated with Inborn genetic diseases (ClinVar).

How common is SRCAP p.Arg1897Gln (c.5690G>A) in the general population?

SRCAP p.Arg1897Gln (c.5690G>A) is very rare (popmax 0.00267%, afr) (gnomAD).

What do computational predictors say about SRCAP p.Arg1897Gln (c.5690G>A)?

AlphaMissense predicts likely pathogenic (score 0.6077) — an in-silico prediction, not a clinical call.

SRCAP p.Arg1897Gln

c.5690G>A · rs771108308 · VCV2231807

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6077 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.6077	likely pathogenic
REVEL	0.383	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.6, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 8,776 bp · p 0.24 · regional, not allelic
Overall
CADD	25.0	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 0.00267% African / African-American · 2/74,910 alleles

Filtering AF 0.000443% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000211%

Overall 0.000682% 11/1,613,828 alleles · very rare exomes 10/1,461,696 · genomes 1/152,132 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00267%	37,455
East Asian	0.00223%	44,888
European (non-Finnish)	0.000678%	147,485

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.Arg1897Gln
Coding: c.5690G>A
MANE Select: NM_006662
dbSNP: rs771108308
Type: single nucleotide variant
Location: chr16:30728997 (GRCh38)
Gene constraint: LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 1897: an α-helix; 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.Arg1897Leu Uncertain significance ★ same residue
SRCAP p.Arg1897Trp Uncertain significance ★ same residue
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

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-arg1897gln (accessed [today's date]).

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