Is GPR152 p.Pro16= (c.48C>T) pathogenic?

GPR152 p.Pro16= (c.48C>T) is classified Likely benign in GPR152 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-01). Rare (popmax 0.162%, amr).

How common is GPR152 p.Pro16= (c.48C>T) in the general population?

GPR152 p.Pro16= (c.48C>T) is rare (popmax 0.162%, amr) (gnomAD).

GPR152 p.Pro16=

c.48C>T · VCV4821310

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.162%, amr)

⚠ 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 1.6	GERP 0.14, phastCons 1
Overall
CADD	5.16	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.162% Admixed American · 96/59,088 alleles

Filtering AF 0.136% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.126%

Overall 0.00637% 102/1,600,884 alleles · rare exomes 45/1,448,536 · genomes 57/152,348 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.162%	615
African / African-American	0.00535%	18,705
Remaining individualsnot grpmax-eligible	0.00323%	30,919

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.Pro16=
Coding: c.48C>T
MANE Select: NM_206997
Type: single nucleotide variant
Location: chr11:67452677 (GRCh38)

Full GPR152 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/gpr152-p-pro16 (accessed [today's date]).

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