Is THAP11 p.Val307= (c.921C>T) pathogenic?

THAP11 p.Val307= (c.921C>T) is classified Likely benign in THAP11 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-26). Rare (popmax 0.215%, mid).

How common is THAP11 p.Val307= (c.921C>T) in the general population?

THAP11 p.Val307= (c.921C>T) is rare (popmax 0.215%, mid) (gnomAD).

THAP11 p.Val307=

c.921C>T · rs369756211 · VCV2041366

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.215%, mid)

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 0.24	GERP -0.57, phastCons 0.98
Overall
CADD	10.13	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.215% Middle Eastern · 13/6,052 alleles

Filtering AF 0.127% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.101%

Overall 0.0161% 259/1,611,844 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.215%	466
South Asian	0.0969%	1,032
Admixed American	0.0651%	1,536
Remaining individualsnot grpmax-eligible	0.0384%	2,601
African / African-American	0.012%	8,339
European (non-Finnish)	0.0073%	13,707

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.Val307=
Coding: c.921C>T
MANE Select: NM_025082 · reported on NM_020457
dbSNP: rs369756211
Type: single nucleotide variant
Location: chr16:67843475 (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-val307 (accessed [today's date]).

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