Is THAP11 p.Phe80= (c.240C>T) pathogenic?

THAP11 p.Phe80= (c.240C>T) is classified Benign in THAP11 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-25). Low-frequency (popmax 1.89%, eas).

How common is THAP11 p.Phe80= (c.240C>T) in the general population?

THAP11 p.Phe80= (c.240C>T) is low-frequency (popmax 1.89%, eas) (gnomAD).

THAP11 p.Phe80=

c.240C>T · rs188675529 · VCV2046828

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.89%, eas)

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 0.4	GERP -1.8, phastCons 0.99
Overall
CADD	12.86	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.89% East Asian · 846/44,700 alleles

Filtering AF 1.79% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.74%

Overall 0.0588% 948/1,611,282 alleles · low-frequency

Ancestry group	Frequency	1 in
East Asiangrpmax	1.89%	53
Remaining individualsnot grpmax-eligible	0.0834%	1,199
South Asian	0.0319%	3,133
Middle Eastern	0.0167%	5,976
Admixed American	0.0167%	5,977
European (non-Finnish)	0.000848%	117,918

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.Phe80=
Coding: c.240C>T
MANE Select: NM_025082 · reported on NM_020457
dbSNP: rs188675529
Type: single nucleotide variant
Location: chr16:67842794 (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-phe80 (accessed [today's date]).

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