Is THAP11 p.Val40= (c.120G>A) pathogenic?

THAP11 p.Val40= (c.120G>A) is classified Likely benign in THAP11 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-29). Ultra-rare (popmax 0.0476%, amr).

How common is THAP11 p.Val40= (c.120G>A) in the general population?

THAP11 p.Val40= (c.120G>A) is ultra-rare (popmax 0.0476%, amr) (gnomAD).

THAP11 p.Val40=

c.120G>A · rs1131526 · VCV2075484

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0476%, amr)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

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 3.8	GERP 0.67, phastCons 1
Overall
CADD	12.38	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0476% Admixed American · 26/54,670 alleles

Filtering AF 0.0333% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0321%

Overall 0.0296% 466/1,575,510 alleles · ultra-rare exomes 424/1,423,212 · genomes 42/152,298 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0476%	2,103
European (non-Finnish)	0.0361%	2,768
Remaining individualsnot grpmax-eligible	0.023%	4,354
African / African-American	0.00946%	10,573

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: THAP11
Protein: p.Val40=
Coding: c.120G>A
MANE Select: NM_020457
dbSNP: rs1131526
Type: single nucleotide variant
Location: chr16:67842674 (GRCh38)

Full THAP11 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/thap11-p-val40 (accessed [today's date]).

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