Is GPR152 p.Ala467Glu (c.1400C>A) pathogenic?

GPR152 p.Ala467Glu (c.1400C>A) is classified Uncertain significance in GPR152 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-14). AlphaMissense: likely benign (0.0839); No allele count reported in gnomAD v4.1 (AN 1,572,054).

How common is GPR152 p.Ala467Glu (c.1400C>A) in the general population?

GPR152 p.Ala467Glu (c.1400C>A) is no allele count reported in gnomAD v4.1 (AN 1,572,054) (gnomAD).

What do computational predictors say about GPR152 p.Ala467Glu (c.1400C>A)?

AlphaMissense predicts likely benign (score 0.0839) — an in-silico prediction, not a clinical call.

GPR152 p.Ala467Glu

c.1400C>A · VCV4673148

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0839 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,572,054)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0839	likely benign
REVEL	0.036	moderately benign-leaning
SaProt	LLR -6.43	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.1	GERP -1.6
Regional constraint	o/e 0.89	unconstrained · MANE · 1,409 bp · p 0.0061 · regional, not allelic
Overall
CADD	15.12	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,572,054). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: GPR152
Protein: p.Ala467Glu
Coding: c.1400C>A
MANE Select: NM_206997
Type: single nucleotide variant
Location: chr11:67451325 (GRCh38)
Gene constraint: LOEUF 1.883 · pLI 0.30 (gnomAD)
Structure: AlphaFold pLDDT 71.72
Residue 467: the 'disordered' region

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-ala467glu (accessed [today's date]).

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