Is STAP1 p.Thr58= (c.174C>T) pathogenic?

STAP1 p.Thr58= (c.174C>T) is classified Likely benign in STAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-13). Ultra-rare (popmax 0.0134%, eas).

How common is STAP1 p.Thr58= (c.174C>T) in the general population?

STAP1 p.Thr58= (c.174C>T) is ultra-rare (popmax 0.0134%, eas) (gnomAD).

STAP1 p.Thr58=

c.174C>T · rs575858699 · VCV1779362

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0134%, eas)

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 -20	GERP -2.9
Overall
CADD	0.154	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0134% East Asian · 6/44,764 alleles

Filtering AF 0.0058% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00395%

Overall 0.00361% 58/1,608,066 alleles · ultra-rare exomes 52/1,455,930 · genomes 6/152,136 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0134%	7,461
African / African-American	0.00401%	24,937
European (non-Finnish)	0.00392%	25,541
Remaining individualsnot grpmax-eligible	0.00321%	31,146
Admixed American	0.00167%	59,894

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.Thr58=
Coding: c.174C>T
MANE Select: NM_012108
dbSNP: rs575858699
Type: single nucleotide variant
Location: chr4:67571137 (GRCh38)
Structure: AlphaFold pLDDT 88.06

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

Similar variants

STAP1 p.Thr58Asn Uncertain significance ★ ⚠ same residue
STAP1 p.Thr58Ile Uncertain significance ★ ⚠ 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-thr58 (accessed [today's date]).

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