Is SMARCA5 p.Pro13Ser (c.37C>T) pathogenic?

SMARCA5 p.Pro13Ser (c.37C>T) is classified Uncertain significance in SMARCA5 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-23). AlphaMissense: likely benign (0.069); Ultra-rare (popmax 0.0129%, amr); Associated with Inborn genetic diseases.

What condition is associated with SMARCA5 p.Pro13Ser (c.37C>T)?

SMARCA5 p.Pro13Ser (c.37C>T) is associated with Inborn genetic diseases (ClinVar).

How common is SMARCA5 p.Pro13Ser (c.37C>T) in the general population?

SMARCA5 p.Pro13Ser (c.37C>T) is ultra-rare (popmax 0.0129%, amr) (gnomAD).

What do computational predictors say about SMARCA5 p.Pro13Ser (c.37C>T)?

AlphaMissense predicts likely benign (score 0.069) — an in-silico prediction, not a clinical call.

SMARCA5 p.Pro13Ser

c.37C>T · VCV3320779

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.069 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0129%, amr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
AlphaMissense	0.069	likely benign
REVEL	0.322	indeterminate
SaProt	LLR -7.06	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.23	GERP 0.45, phastCons 0.98
Regional constraint	o/e 1.28	unconstrained · MANE · 7,517 bp · p 0.0017 · regional, not allelic
Overall
CADD	17.35	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0129% Admixed American · 7/54,394 alleles

Filtering AF 0.00603% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00422%

Overall 0.000901% 14/1,554,204 alleles · ultra-rare exomes 10/1,401,822 · genomes 4/152,382 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0129%	7,771
East Asian	0.00238%	41,938
Remaining individualsnot grpmax-eligible	0.00165%	60,636
European (non-Finnish)	0.000432%	231,441

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: SMARCA5
Protein: p.Pro13Ser
Coding: c.37C>T
MANE Select: NM_003601
Type: single nucleotide variant
Location: chr4:143513961 (GRCh38)

Full SMARCA5 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

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/smarca5-p-pro13ser (accessed [today's date]).

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