Is GPR34 p.Val296= (c.888A>G) pathogenic?

GPR34 p.Val296= (c.888A>G) is classified Benign in GPR34 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-03-28). Low-frequency (popmax 1.33%, mid).

How common is GPR34 p.Val296= (c.888A>G) in the general population?

GPR34 p.Val296= (c.888A>G) is low-frequency (popmax 1.33%, mid) (gnomAD).

GPR34 p.Val296=

c.888A>G · rs138580045 · VCV713839

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.33%, mid)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.14	GERP -1.9
Overall
CADD	1.282	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.33% Middle Eastern · 58/4,345 alleles

Filtering AF 1.06% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.961%

Overall 0.271% 3,273/1,206,888 alleles · low-frequency exomes 3,050/1,094,665 · genomes 223/112,223 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	1.33%	75
European (non-Finnish)	0.319%	314
Finnishnot grpmax-eligible	0.267%	375
Remaining individualsnot grpmax-eligible	0.263%	380
Admixed American	0.142%	703
South Asian	0.0582%	1,720
Ashkenazi Jewishnot grpmax-eligible	0.0409%	2,444
African / African-American	0.0262%	3,822

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: GPR34
Protein: p.Val296=
Coding: c.888A>G
MANE Select: NM_001097579
dbSNP: rs138580045
Type: single nucleotide variant
Location: chrX:41696521 (GRCh38)

Full GPR34 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/gpr34-p-val296 (accessed [today's date]).

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