Is STUB1 p.Asp291= (c.873C>T) pathogenic?

STUB1 p.Asp291= (c.873C>T) is classified Likely benign in STUB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-23). Ultra-rare (popmax 0.0147%, afr).

How common is STUB1 p.Asp291= (c.873C>T) in the general population?

STUB1 p.Asp291= (c.873C>T) is ultra-rare (popmax 0.0147%, afr) (gnomAD).

STUB1 p.Asp291=

c.873C>T · rs200457699 · VCV2181986

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0147%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -3.6	GERP -3.1
Overall
CADD	0.32	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0147% African / African-American · 11/75,064 alleles

Filtering AF 0.00814% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00632%

Overall 0.00161% 26/1,613,484 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0147%	6,824
South Asian	0.00439%	22,772
Remaining individualsnot grpmax-eligible	0.0032%	31,248
East Asian	0.00223%	44,886
Admixed American	0.00167%	60,030
European (non-Finnish)	0.000593%	168,574

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: STUB1
Protein: p.Asp291=
Coding: c.873C>T
MANE Select: NM_001005920 · reported on NM_005861
dbSNP: rs200457699
Type: single nucleotide variant
Location: chr16:682450 (GRCh38)

Full STUB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/stub1-p-asp291 (accessed [today's date]).

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