Is SMARCC1 p.Pro293= (c.879T>C) pathogenic?

SMARCC1 p.Pro293= (c.879T>C) is classified Likely benign in SMARCC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-04-27). Ultra-rare (popmax 0.012%, afr); Associated with Inborn genetic diseases.

What condition is associated with SMARCC1 p.Pro293= (c.879T>C)?

SMARCC1 p.Pro293= (c.879T>C) is associated with Inborn genetic diseases (ClinVar).

How common is SMARCC1 p.Pro293= (c.879T>C) in the general population?

SMARCC1 p.Pro293= (c.879T>C) is ultra-rare (popmax 0.012%, afr) (gnomAD).

SMARCC1 p.Pro293=

c.879T>C · VCV4864846

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.012%, afr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>C here scores Δ0.73 · evaluated, not missing
Constraint at this position
Conservation	phyloP -1.3	GERP -4.8
Overall
CADD	6.244	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.012% African / African-American · 9/74,926 alleles

Filtering AF 0.00623% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00468%

Overall 0.000806% 13/1,613,610 alleles · ultra-rare exomes 9/1,461,446 · genomes 4/152,164 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.012%	8,325
Remaining individualsnot grpmax-eligible	0.0064%	15,616

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: SMARCC1
Protein: p.Pro293=
Coding: c.879T>C
MANE Select: NM_003074
Type: single nucleotide variant
Location: chr3:47710722 (GRCh38)
Gene constraint: LOEUF 0.369 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 66.98 · 5 PDB
Residue 293: a UniProt-annotated variant site (in hyc5); the 'marr-like, brct and chromo domains module' region

Full SMARCC1 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

SMARCC1 p.Arg1032His Uncertain significance ★★ ⚠ same condition
SMARCC1 p.Gln538His Uncertain significance ★★ ⚠ same condition
SMARCC1 p.Met151Val Uncertain significance ★★ ⚠ same condition
SMARCC1 p.Ser54Leu Uncertain significance ★★ ⚠ same condition
SMARCC1 p.Arg144Ter Pathogenic ★ same condition
SMARCC1 p.Ala1096Val Uncertain significance ★ ⚠ same condition
SMARCC1 p.Ala202Ser Uncertain significance ★ ⚠ same condition
SMARCC1 p.Ala24Val 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/smarcc1-p-pro293 (accessed [today's date]).

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