Is SMARCA4 p.Pro269= (c.807C>T) pathogenic?

SMARCA4 p.Pro269= (c.807C>T) is classified Likely benign in SMARCA4 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-06). Ultra-rare (popmax 0.0165%, mid); Associated with hereditary neoplastic syndrome.

What condition is associated with SMARCA4 p.Pro269= (c.807C>T)?

SMARCA4 p.Pro269= (c.807C>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is SMARCA4 p.Pro269= (c.807C>T) in the general population?

SMARCA4 p.Pro269= (c.807C>T) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

SMARCA4 p.Pro269=

c.807C>T · VCV3445959

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.39	GERP -0.53, phastCons 0.99
Overall
CADD	7.73	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,060 alleles

Overall 6.21e-05% 1/1,610,838 alleles · ultra-rare exomes 1/1,458,548 · genomes 0/152,290 · 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: SMARCA4
Protein: p.Pro269=
Coding: c.807C>T
MANE Select: NM_003072
Type: single nucleotide variant
Location: chr19:10986951 (GRCh38)
Gene constraint: LOEUF 0.226 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 65.38 · 31 PDB
Residue 269: the 'necessary for interaction with ss18l1/crest' region; the 'disordered' region

Full SMARCA4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SMARCA4 p.Pro269Leu Uncertain significance ★★ ⚠ same residue
SMARCA4 p.Pro269Arg Uncertain significance ★ same residue
SMARCA4 p.Pro269His Uncertain significance ★ ⚠ same residue
SMARCA4 p.Pro269Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
SMARCA4 p.Pro269Thr Uncertain significance ★ ⚠ same residue
SMARCA4 c.1943+1G>A Likely pathogenic ★★ same condition
SMARCA4 c.2438+1G>A Pathogenic/Likely pathogenic ★★ same condition
SMARCA4 c.3216-1G>C Likely pathogenic ★★ 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/smarca4-p-pro269 (accessed [today's date]).

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