Is ENTPD7 p.Pro438fs (c.1311del) pathogenic?

ENTPD7 p.Pro438fs (c.1311del) is classified Uncertain significance in ENTPD7 (ClinVar, Single submitter, 1 submitter; last evaluated 2015-07-30). Ultra-rare (popmax 0.0741%, nfe).

How common is ENTPD7 p.Pro438fs (c.1311del) in the general population?

ENTPD7 p.Pro438fs (c.1311del) is ultra-rare (popmax 0.0741%, nfe) (gnomAD).

ENTPD7 p.Pro438fs

c.1311del · rs879255416 · VCV252727

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

ultra-rare (popmax 0.0741%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -15	GERP -4.3
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0741% European (non-Finnish) · 871/1,175,044 alleles

Filtering AF 0.07% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0684%

Overall 0.0682% 1,095/1,606,238 alleles · ultra-rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.293%	342
European (non-Finnish)grpmax	0.0741%	1,349
Remaining individualsnot grpmax-eligible	0.0467%	2,142
Middle Eastern	0.0166%	6,022
African / African-American	0.00535%	18,692
South Asian	0.00222%	45,126
Admixed American	0.00169%	59,284

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: ENTPD7
Protein: p.Pro438fs
Coding: c.1311del
MANE Select: NM_078470 · reported on NM_020354
dbSNP: rs879255416
Type: Deletion
Location: chr10:99698832 (GRCh38)

Full ENTPD7 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/entpd7-p-pro438fs (accessed [today's date]).

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