Is SRCAP p.Ala1807Val (c.5420C>T) pathogenic?

SRCAP p.Ala1807Val (c.5420C>T) is classified Likely benign in SRCAP (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-02-01). AlphaMissense: likely benign (0.1125); Ultra-rare (popmax 0.0533%, nfe).

How common is SRCAP p.Ala1807Val (c.5420C>T) in the general population?

SRCAP p.Ala1807Val (c.5420C>T) is ultra-rare (popmax 0.0533%, nfe) (gnomAD).

What do computational predictors say about SRCAP p.Ala1807Val (c.5420C>T)?

AlphaMissense predicts likely benign (score 0.1125) — an in-silico prediction, not a clinical call.

SRCAP p.Ala1807Val

c.5420C>T · rs150467782 · VCV286326

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.1125 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0533%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Computational evidence

Protein change
AlphaMissense	0.1125	likely benign
REVEL	0.158	moderately benign-leaning
SaProt	—	not scored · why
⇒ AlphaMissense and REVEL both call this tolerated; SaProt makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.3	GERP 1.5, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 8,776 bp · p 0.24 · regional, not allelic
Overall
CADD	22.1	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

Grpmax group 0.0533% European (non-Finnish) · 629/1,179,924 alleles

Filtering AF 0.0498% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0484%

Overall 0.0449% 725/1,614,016 alleles · ultra-rare exomes 667/1,461,724 · genomes 58/152,292 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0533%	1,876
Remaining individualsnot grpmax-eligible	0.0416%	2,403
Admixed American	0.035%	2,858
South Asian	0.0264%	3,795
Finnishnot grpmax-eligible	0.0219%	4,572
African / African-American	0.0133%	7,504
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,606

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.Ala1807Val
Coding: c.5420C>T
MANE Select: NM_006662
dbSNP: rs150467782
Type: single nucleotide variant
Location: chr16:30724844 (GRCh38)
Gene constraint: LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 1807: a UniProt-annotated variant site (in dehmba)

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

Similar variants

SRCAP p.Ala1807Ser Uncertain significance ★ ⚠ same residue
SRCAP p.Arg2329Ter Pathogenic/Likely pathogenic ★★ same type
SRCAP p.Arg2435Ter Pathogenic/Likely pathogenic ★★ same type
SRCAP p.Arg2444Ter Pathogenic ★★ same type
SRCAP p.Arg2718Ter Pathogenic/Likely pathogenic ★★ same type
SRCAP p.Arg2748Ter Pathogenic ★★ same type
SRCAP p.Gln2407Ter Pathogenic ★★ same type
SRCAP p.Gln2419Ter Pathogenic ★★ same type

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-ala1807val (accessed [today's date]).

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