Is GPR152 p.Val151Phe (c.451G>T) pathogenic?

GPR152 p.Val151Phe (c.451G>T) is classified Uncertain significance in GPR152 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-29). AlphaMissense: likely benign (0.1431); Very rare (popmax 0.00167%, amr).

How common is GPR152 p.Val151Phe (c.451G>T) in the general population?

GPR152 p.Val151Phe (c.451G>T) is very rare (popmax 0.00167%, amr) (gnomAD).

What do computational predictors say about GPR152 p.Val151Phe (c.451G>T)?

AlphaMissense predicts likely benign (score 0.1431) — an in-silico prediction, not a clinical call.

GPR152 p.Val151Phe

c.451G>T · VCV4031474

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1431 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1431	likely benign
REVEL	0.215	benign-leaning
SaProt	LLR -10.88	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.9	GERP 0.19, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 1,409 bp · p 0.0061 · regional, not allelic
Overall
CADD	23.3	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/60,018 alleles

Overall 6.21e-05% 1/1,611,348 alleles · very rare exomes 1/1,459,014 · genomes 0/152,334 · 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: GPR152
Protein: p.Val151Phe
Coding: c.451G>T
MANE Select: NM_206997
Type: single nucleotide variant
Location: chr11:67452274 (GRCh38)
Gene constraint: LOEUF 1.883 · pLI 0.30 (gnomAD)
Structure: AlphaFold pLDDT 71.72

Full GPR152 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GPR152 p.Ala124Thr Uncertain significance ★ ⚠ same type
GPR152 p.Ala133Val Uncertain significance ★ ⚠ same type
GPR152 p.Ala153Thr Uncertain significance ★ ⚠ same type
GPR152 p.Ala217Thr Uncertain significance ★ ⚠ same type
GPR152 p.Ala230Glu Uncertain significance ★ ⚠ same type
GPR152 p.Ala231Pro Uncertain significance ★ ⚠ same type
GPR152 p.Ala236Asp Uncertain significance ★ ⚠ same type
GPR152 p.Ala314Thr 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/gpr152-p-val151phe (accessed [today's date]).

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