Is GP6 p.Arg162= (c.484A>C) pathogenic?

GP6 p.Arg162= (c.484A>C) is classified Benign in GP6 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-02-04). Common (popmax 98.1%, eas) — too common for a highly-penetrant pathogenic allele; Associated with platelet-type bleeding disorder 11.

What condition is associated with GP6 p.Arg162= (c.484A>C)?

GP6 p.Arg162= (c.484A>C) is associated with platelet-type bleeding disorder 11 (ClinVar).

GP6 p.Arg162=

Q: How common is GP6 p.Arg162= (c.484A>C) in the general population?

GP6 p.Arg162= (c.484A>C) is common (popmax 98.1%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.484A>C · rs892090 · VCV257418

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Common

common (popmax 98.1%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

platelet-type bleeding disorder 11

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 -0.12	GERP -4.1
Overall
CADD	7.322	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 98.1% East Asian · 43,990/44,856 alleles

Filtering AF 97.3% ClinGen BA1/BS1 input FAF95, joint · FAF99 97%

Overall 84% 1,354,282/1,611,948 alleles · common exomes 1,227,329/1,459,760 · genomes 126,953/152,188 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	98.1%	1
Admixed American	91.4%	1
Finnishnot grpmax-eligible	88.4%	1
Remaining individualsnot grpmax-eligible	84%	1
European (non-Finnish)	83.9%	1
Middle Eastern	80.5%	1
Ashkenazi Jewishnot grpmax-eligible	79.5%	1
South Asian	78.9%	1
Amishnot grpmax-eligible	77%	1
African / African-American	76.9%	1

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.Arg162=
Coding: c.484A>C
MANE Select: NM_016363
dbSNP: rs892090
Type: single nucleotide variant
Location: chr19:55027704 (GRCh38)
Gene constraint: LOEUF 1.734 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 76.52 · 6 PDB
Residue 162: a β-strand; the ig-like c2-type 2 domain

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

Disease context

platelet-type bleeding disorder 11 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GP6 c.*395C>T Benign ★★ same condition
GP6 c.*485C>T Likely benign ★★ same condition
GP6 c.*693A>G Benign ★★ same condition
GP6 c.*792T>C Benign ★★ same condition
GP6 p.Ala249Thr Benign ★★ same condition
GP6 p.Glu237Lys Benign ★★ same condition
GP6 p.Leu312= Benign ★★ same condition
GP6 p.Leu317Gln Benign ★★ same condition

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-arg162 (accessed [today's date]).

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