Is GPR179 p.Arg792Lys (c.2375G>A) pathogenic?

GPR179 p.Arg792Lys (c.2375G>A) is classified Uncertain significance in GPR179 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-16). AlphaMissense: likely benign (0.1545); Very rare (popmax 0.000509%, nfe); Associated with Inborn genetic diseases.

What condition is associated with GPR179 p.Arg792Lys (c.2375G>A)?

GPR179 p.Arg792Lys (c.2375G>A) is associated with Inborn genetic diseases (ClinVar).

How common is GPR179 p.Arg792Lys (c.2375G>A) in the general population?

GPR179 p.Arg792Lys (c.2375G>A) is very rare (popmax 0.000509%, nfe) (gnomAD).

What do computational predictors say about GPR179 p.Arg792Lys (c.2375G>A)?

AlphaMissense predicts likely benign (score 0.1545) — an in-silico prediction, not a clinical call.

GPR179 p.Arg792Lys

c.2375G>A · VCV4031615

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1545 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000509%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1545	likely benign
REVEL	0.054	moderately benign-leaning
SaProt	—	withheld · numbering disagrees past residue 493 · why
⇒ AlphaMissense and REVEL both call this tolerated; SaProt makes no call.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 4	GERP 2.6, phastCons 1
Overall
CADD	20.6	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 is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000509% European (non-Finnish) · 6/1,178,644 alleles

Filtering AF 0.000183% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00012%

Overall 0.000373% 6/1,608,180 alleles · very rare exomes 2/1,455,936 · genomes 4/152,244 · 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: GPR179
Protein: p.Arg792Lys
Coding: c.2375G>A
MANE Select: NM_001004334
Type: single nucleotide variant
Location: chr17:38331194 (GRCh38)
Gene constraint: LOEUF 0.965 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 43.22 · 2 PDB
Residue 792: the 'disordered' region

Full GPR179 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GPR179 p.Arg792= Likely benign ★ same residue
GPR179 p.Ala106Ser Uncertain significance ★★ ⚠ same condition
GPR179 p.Ala1143Thr Uncertain significance ★★ ⚠ same condition
GPR179 p.Ala1236Thr Uncertain significance ★★ ⚠ same condition
GPR179 p.Ala1460Thr Uncertain significance ★★ ⚠ same condition
GPR179 p.Ala1588Val Uncertain significance ★★ ⚠ same condition
GPR179 p.Ala1702Glu Uncertain significance ★★ ⚠ same condition
GPR179 p.Ala1995Thr Uncertain significance ★★ ⚠ same condition

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/gpr179-p-arg792lys (accessed [today's date]).

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