Is SRCAP p.Arg1007Gln (c.3020G>A) pathogenic?

SRCAP p.Arg1007Gln (c.3020G>A) is classified Uncertain significance in SRCAP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-09-18). AlphaMissense: ambiguous (0.3487); Very rare (popmax 0.00503%, amr); Associated with Inborn genetic diseases.

What condition is associated with SRCAP p.Arg1007Gln (c.3020G>A)?

SRCAP p.Arg1007Gln (c.3020G>A) is associated with Inborn genetic diseases (ClinVar).

How common is SRCAP p.Arg1007Gln (c.3020G>A) in the general population?

SRCAP p.Arg1007Gln (c.3020G>A) is very rare (popmax 0.00503%, amr) (gnomAD).

What do computational predictors say about SRCAP p.Arg1007Gln (c.3020G>A)?

AlphaMissense predicts ambiguous (score 0.3487) — an in-silico prediction, not a clinical call.

SRCAP p.Arg1007Gln

c.3020G>A · VCV3322572

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.3487 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00503%, amr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3487	ambiguous
REVEL	0.566	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 2.7, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 8,776 bp · p 0.24 · regional, not allelic
Overall
CADD	26.3	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 0.00503% Admixed American · 3/59,684 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000972%

Overall 0.00155% 25/1,611,690 alleles · very rare exomes 21/1,459,606 · genomes 4/152,084 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00503%	19,895
European (non-Finnish)	0.00178%	56,134
South Asian	0.0011%	90,838

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.Arg1007Gln
Coding: c.3020G>A
MANE Select: NM_006662
Type: single nucleotide variant
Location: chr16:30720745 (GRCh38)
Gene constraint: LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 1007: 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.Arg1007Trp 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
SRCAP p.Ala2699Val 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-arg1007gln (accessed [today's date]).

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