Is STAP1 p.Arg36Trp (c.106C>T) pathogenic?

STAP1 p.Arg36Trp (c.106C>T) is classified Uncertain significance in STAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-21). AlphaMissense: likely benign (0.2686); Very rare (popmax 0.00223%, eas).

How common is STAP1 p.Arg36Trp (c.106C>T) in the general population?

STAP1 p.Arg36Trp (c.106C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

What do computational predictors say about STAP1 p.Arg36Trp (c.106C>T)?

AlphaMissense predicts likely benign (score 0.2686) — an in-silico prediction, not a clinical call.

STAP1 p.Arg36Trp

c.106C>T · rs201298373 · VCV1782948

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2686 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2686	likely benign
REVEL	0.279	benign-leaning
SaProt	LLR -10.10	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.26	GERP -3.8, phastCons 0.97
Overall
CADD	18.09	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 0.00223% East Asian · 1/44,828 alleles

Filtering AF 0.000292% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000211%

Overall 0.000744% 12/1,612,034 alleles · very rare exomes 11/1,459,992 · genomes 1/152,042 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.00313%	31,971
East Asiangrpmax	0.00223%	44,828
South Asian	0.0011%	90,802
European (non-Finnish)	0.000679%	147,370

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Arg36Trp
Coding: c.106C>T
MANE Select: NM_012108
dbSNP: rs201298373
Type: single nucleotide variant
Location: chr4:67558915 (GRCh38)
Structure: AlphaFold pLDDT 88.06

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

Similar variants

STAP1 p.Arg36Gln Uncertain significance ★ ⚠ same residue
STAP1 p.Arg36= Likely benign ★ same residue
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

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-arg36trp (accessed [today's date]).

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