Is GPR88 p.Phe293= (c.879C>T) pathogenic?

GPR88 p.Phe293= (c.879C>T) is classified Likely benign in GPR88 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-05-02). Very rare (popmax 0.000128%).

How common is GPR88 p.Phe293= (c.879C>T) in the general population?

GPR88 p.Phe293= (c.879C>T) is very rare (popmax 0.000128%) (gnomAD).

GPR88 p.Phe293=

c.879C>T · VCV3606395

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.000128%)

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	GERP -0.73, phastCons 1
Overall
CADD	9.959	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000128%

Overall 0.000128% 2/1,559,934 alleles · very rare exomes 2/1,408,034 · genomes 0/151,900 · joint denominator

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: GPR88
Protein: p.Phe293=
Coding: c.879C>T
MANE Select: NM_022049
Type: single nucleotide variant
Location: chr1:100539845 (GRCh38)
Gene constraint: LOEUF 1.77 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.73 · 2 PDB
Residue 293: a UniProt-annotated variant site (in cocpmr; uncertain significance); an α-helix

Full GPR88 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GPR88 p.Ala263Gly Uncertain significance ★★ ⚠ same type
GPR88 p.Arg30Gln Uncertain significance ★★ ⚠ same type
GPR88 p.Leu375Val Uncertain significance ★★ ⚠ same type
GPR88 p.Pro102Ser Uncertain significance ★★ ⚠ same type
GPR88 p.Pro256Leu Uncertain significance ★★ ⚠ same type
GPR88 p.Pro274Ser Uncertain significance ★★ ⚠ same type
GPR88 p.Thr96Ile Uncertain significance ★★ ⚠ same type
GPR88 p.Val317Met 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/gpr88-p-phe293 (accessed [today's date]).

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