Is SMARCA2 p.Pro267Ser (c.799C>T) pathogenic?

SMARCA2 p.Pro267Ser (c.799C>T) is classified Uncertain significance in SMARCA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-11). AlphaMissense: likely benign (0.06); Very rare (popmax 0.00451%, sas); Associated with Inborn genetic diseases.

What condition is associated with SMARCA2 p.Pro267Ser (c.799C>T)?

SMARCA2 p.Pro267Ser (c.799C>T) is associated with Inborn genetic diseases (ClinVar).

How common is SMARCA2 p.Pro267Ser (c.799C>T) in the general population?

SMARCA2 p.Pro267Ser (c.799C>T) is very rare (popmax 0.00451%, sas) (gnomAD).

What do computational predictors say about SMARCA2 p.Pro267Ser (c.799C>T)?

AlphaMissense predicts likely benign (score 0.06) — an in-silico prediction, not a clinical call.

SMARCA2 p.Pro267Ser

c.799C>T · rs1819895639 · VCV2278208

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.06 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00451%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.06	likely benign
REVEL	0.138	moderately benign-leaning
SaProt	LLR -6.23	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.78	GERP -1.5, phastCons 0.038
Regional constraint	o/e 1.18	unconstrained · MANE · 7,571 bp · p 0.073 · regional, not allelic
Overall
CADD	18.0	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 0.00451% South Asian · 1/22,156 alleles

Overall 9.9e-05% 1/1,009,640 alleles · very rare exomes 0/861,986 · genomes 1/147,654 · 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: SMARCA2
Protein: p.Pro267Ser
Coding: c.799C>T
MANE Select: NM_003070
dbSNP: rs1819895639
Type: single nucleotide variant
Location: chr9:2047237 (GRCh38)
Gene constraint: LOEUF 0.317 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 66.06 · 32 PDB
Residue 267: the 'disordered' region

Full SMARCA2 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

SMARCA2 p.Pro267Arg Uncertain significance ★ ⚠ same residue
SMARCA2 p.Ala1138Pro Pathogenic/Likely pathogenic ★★ same condition
SMARCA2 p.Arg505Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
SMARCA2 p.Ala1215Val Uncertain significance ★★ ⚠ same condition
SMARCA2 p.Ala1389Ser Uncertain significance ★★ ⚠ same condition
SMARCA2 p.Arg1266Gly Uncertain significance ★★ ⚠ same condition
SMARCA2 p.Arg427Cys Uncertain significance ★★ ⚠ same condition
SMARCA2 p.Glu1509Asp 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/smarca2-p-pro267ser (accessed [today's date]).

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