Is SMARCA4 p.Pro30Ser (c.88C>T) pathogenic?

SMARCA4 p.Pro30Ser (c.88C>T) is classified Uncertain significance in SMARCA4 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-10-05). AlphaMissense: likely benign (0.1844); Absent from gnomAD v4.1; Associated with intellectual disability, autosomal dominant 16.

What condition is associated with SMARCA4 p.Pro30Ser (c.88C>T)?

SMARCA4 p.Pro30Ser (c.88C>T) is associated with intellectual disability, autosomal dominant 16, rhabdoid tumor predisposition syndrome 2, hereditary neoplastic syndrome (ClinVar).

How common is SMARCA4 p.Pro30Ser (c.88C>T) in the general population?

SMARCA4 p.Pro30Ser (c.88C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SMARCA4 p.Pro30Ser (c.88C>T)?

AlphaMissense predicts likely benign (score 0.1844) — an in-silico prediction, not a clinical call.

SMARCA4 p.Pro30Ser

c.88C>T · rs1599928968 · VCV649569

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1844 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

intellectual disability, autosomal dominant 16

Computational evidence

Protein change
AlphaMissense	0.1844	likely benign
REVEL	0.463	indeterminate
SaProt	LLR -9.52	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.2, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 2,200 bp · p 0.0027 · regional, not allelic
Overall
CADD	25.7	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SMARCA4
Protein: p.Pro30Ser
Coding: c.88C>T
MANE Select: NM_003072
dbSNP: rs1599928968
Type: single nucleotide variant
Location: chr19:10984239 (GRCh38)
Gene constraint: LOEUF 0.226 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 65.38 · 31 PDB
Residue 30: 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

intellectual disability, autosomal dominant 16 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: rhabdoid tumor predisposition syndrome 2 hereditary neoplastic syndrome

Similar variants

SMARCA4 p.Pro30Arg Uncertain significance ★★ ⚠ same residue
SMARCA4 p.Pro30Ala Uncertain significance ★ ⚠ same residue
SMARCA4 p.Pro30Leu Uncertain significance ★ same residue
SMARCA4 p.Pro30= Likely benign ★ same residue
SMARCA4 c.1943+1G>A Likely pathogenic ★★ same condition
SMARCA4 c.2274+1G>T 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-pro30ser (accessed [today's date]).

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