Is GP6 p.Pro24= (c.72G>A) pathogenic?

GP6 p.Pro24= (c.72G>A) is classified Likely benign in GP6 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-06-12). Ultra-rare (popmax 0.0468%, amr).

How common is GP6 p.Pro24= (c.72G>A) in the general population?

GP6 p.Pro24= (c.72G>A) is ultra-rare (popmax 0.0468%, amr) (gnomAD).

GP6 p.Pro24=

c.72G>A · rs368522136 · VCV3011785

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0468%, amr)

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 -20	GERP -4
Overall
CADD	0.093	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0468% Admixed American · 28/59,832 alleles

Filtering AF 0.0332% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0287%

Overall 0.00353% 57/1,612,474 alleles · ultra-rare exomes 37/1,460,274 · genomes 20/152,200 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0468%	2,137
East Asian	0.00223%	44,866
European (non-Finnish)	0.0022%	45,357
Remaining individualsnot grpmax-eligible	0.0016%	62,400
African / African-American	0.00134%	74,904

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: GP6
Protein: p.Pro24=
Coding: c.72G>A
MANE Select: NM_016363
dbSNP: rs368522136
Type: single nucleotide variant
Location: chr19:55032392 (GRCh38)
Gene constraint: LOEUF 1.734 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 76.52 · 6 PDB

Full GP6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GP6 p.Pro24Leu Uncertain significance ★★ ⚠ same residue
GP6 p.Trp160Ter Pathogenic ★★ same type
GP6 c.*106A>C Uncertain significance ★★ same type
GP6 c.*189C>T Uncertain significance ★★ same type
GP6 c.*304C>T Uncertain significance ★★ same type
GP6 c.*523G>C Uncertain significance ★★ same type
GP6 c.*531T>C Uncertain significance ★★ same type
GP6 c.*820T>C 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/gp6-p-pro24 (accessed [today's date]).

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