Is ANGPTL7 p.Pro23= (c.69A>T) pathogenic?

ANGPTL7 p.Pro23= (c.69A>T) is classified Likely benign in ANGPTL7 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-01). Absent from gnomAD v4.1.

How common is ANGPTL7 p.Pro23= (c.69A>T) in the general population?

ANGPTL7 p.Pro23= (c.69A>T) is absent from gnomAD v4.1 (gnomAD).

ANGPTL7 p.Pro23=

c.69A>T · VCV4681515

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -3.2	GERP -3.5
Overall
CADD	0.479	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ANGPTL7
Protein: p.Pro23=
Coding: c.69A>T
MANE Select: NM_021146
Type: single nucleotide variant
Location: chr1:11189648 (GRCh38)
Gene constraint: LOEUF 1.231 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.45

Full ANGPTL7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ANGPTL7 p.Pro23Ala Likely benign ★ same residue
ANGPTL7 p.Arg176Ser Uncertain significance ★ ⚠ same type
ANGPTL7 p.Arg211Gln Uncertain significance ★ ⚠ same type
ANGPTL7 p.Arg214Ile Uncertain significance ★ ⚠ same type
ANGPTL7 p.Arg218Gln Uncertain significance ★ ⚠ same type
ANGPTL7 p.Arg220His Uncertain significance ★ ⚠ same type
ANGPTL7 p.Arg231Cys Uncertain significance ★ ⚠ same type
ANGPTL7 p.Arg289Cys Uncertain significance ★ ⚠ 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/angptl7-p-pro23 (accessed [today's date]).

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