Is STAP1 p.Ile34Met (c.102C>G) pathogenic?

STAP1 p.Ile34Met (c.102C>G) is classified Likely benign in STAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-01). AlphaMissense: likely benign (0.1703); Rare (popmax 0.964%, sas).

How common is STAP1 p.Ile34Met (c.102C>G) in the general population?

STAP1 p.Ile34Met (c.102C>G) is rare (popmax 0.964%, sas) (gnomAD).

What do computational predictors say about STAP1 p.Ile34Met (c.102C>G)?

AlphaMissense predicts likely benign (score 0.1703) — an in-silico prediction, not a clinical call.

STAP1 p.Ile34Met

c.102C>G · VCV4533761

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1703 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.964%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1703	likely benign
REVEL	0.05	moderately benign-leaning
SaProt	LLR -8.12	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.031	GERP -1.6, phastCons 0.88
Overall
CADD	18.59	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.964% South Asian · 876/90,860 alleles

Filtering AF 0.911% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.89%

Overall 0.0593% 957/1,612,690 alleles · rare exomes 909/1,460,480 · genomes 48/152,210 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.964%	104
Remaining individualsnot grpmax-eligible	0.0689%	1,452
Middle Eastern	0.0331%	3,024
Admixed American	0.00334%	29,938
European (non-Finnish)	0.0028%	35,735
East Asian	0.00223%	44,844

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: STAP1
Protein: p.Ile34Met
Coding: c.102C>G
MANE Select: NM_012108
Type: single nucleotide variant
Location: chr4:67558911 (GRCh38)
Structure: AlphaFold pLDDT 88.06

Full STAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

STAP1 p.Gln192Arg Uncertain significance ★★ ⚠ same type
STAP1 p.Leu288Val Uncertain significance ★★ ⚠ same type
STAP1 c.120+6T>C Benign/Likely benign ★★ same type
STAP1 c.192+102T>C Likely benign ★★ same type
STAP1 c.192+10T>C Benign ★★ same type
STAP1 c.530+11A>G Benign ★★ same type
STAP1 c.530+60A>G Benign ★★ same type
STAP1 c.730-41G>C Benign ★★ same type

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/stap1-p-ile34met (accessed [today's date]).

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