Is GP1BA p.Arg592= (c.1776G>C) pathogenic?

GP1BA p.Arg592= (c.1776G>C) is classified Likely benign in GP1BA (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-31). Absent from gnomAD v4.1.

How common is GP1BA p.Arg592= (c.1776G>C) in the general population?

GP1BA p.Arg592= (c.1776G>C) is absent from gnomAD v4.1 (gnomAD).

GP1BA p.Arg592=

c.1776G>C · VCV4932797

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	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.89	GERP -1.3, phastCons 0.69
Overall
CADD	6.566	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: GP1BA
Protein: p.Arg592=
Coding: c.1776G>C
MANE Select: NM_000173
Type: single nucleotide variant
Location: chr17:4934380 (GRCh38)
Gene constraint: LOEUF 1.289 · pLI 0.10 (gnomAD)
Structure: AlphaFold pLDDT 64.65 · 22 PDB

Full GP1BA gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GP1BA p.Arg592Gln Uncertain significance ★★ ⚠ same residue
GP1BA p.Arg592Trp Uncertain significance ★★ ⚠ same residue
GP1BA p.Arg592fs Uncertain significance ★ same residue
GP1BA p.Cys225Arg Likely pathogenic ★★★ same type
GP1BA p.Cys81Arg Pathogenic ★★★ same type
GP1BA p.Gln346Ter Likely pathogenic ★★★ same type
GP1BA p.Glu347Ter Likely pathogenic ★★★ same type
GP1BA p.Leu145Pro Likely pathogenic ★★★ 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/gp1ba-p-arg592 (accessed [today's date]).

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