Is SMARCB1 p.Arg53= (c.159A>G) pathogenic?

SMARCB1 p.Arg53= (c.159A>G) is classified Likely benign in SMARCB1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-12-15). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with SMARCB1 p.Arg53= (c.159A>G)?

SMARCB1 p.Arg53= (c.159A>G) is associated with hereditary neoplastic syndrome (ClinVar).

How common is SMARCB1 p.Arg53= (c.159A>G) in the general population?

SMARCB1 p.Arg53= (c.159A>G) is absent from gnomAD v4.1 (gnomAD).

SMARCB1 p.Arg53=

c.159A>G · rs2145960255 · VCV1776077

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 1.1	GERP -1.6, phastCons 1
Overall
CADD	10.47	PHRED · no single calibrated threshold — expert panels disagree

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: SMARCB1
Protein: p.Arg53=
Coding: c.159A>G
MANE Select: NM_003073
dbSNP: rs2145960255
Type: single nucleotide variant
Location: chr22:23791821 (GRCh38)
Gene constraint: LOEUF 0.221 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 80.77 · 17 PDB
Residue 53: a β-strand; the 'dna-binding' region

Full SMARCB1 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

SMARCB1 p.Arg53Leu Pathogenic/Likely pathogenic ★★ same residue
SMARCB1 p.Arg53Ter Pathogenic ★★ same residue
SMARCB1 p.Arg53Gln Uncertain significance ★★ ⚠ same residue
SMARCB1 c.795+1G>A Likely pathogenic ★★ same condition
SMARCB1 c.93+1G>A Likely pathogenic ★★ same condition
SMARCB1 c.986+1G>A Likely pathogenic ★★ same condition
SMARCB1 c.*82C>T Pathogenic/Likely pathogenic ★★ same condition
SMARCB1 p.Arg158Ter 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/smarcb1-p-arg53 (accessed [today's date]).

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