Is GDPGP1 p.Arg102Cys (c.304C>T) pathogenic?

GDPGP1 p.Arg102Cys (c.304C>T) is classified Uncertain significance in GDPGP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-02). AlphaMissense: likely pathogenic (0.8346); Ultra-rare (popmax 0.0156%, eas).

How common is GDPGP1 p.Arg102Cys (c.304C>T) in the general population?

GDPGP1 p.Arg102Cys (c.304C>T) is ultra-rare (popmax 0.0156%, eas) (gnomAD).

What do computational predictors say about GDPGP1 p.Arg102Cys (c.304C>T)?

AlphaMissense predicts likely pathogenic (score 0.8346) — an in-silico prediction, not a clinical call.

GDPGP1 p.Arg102Cys

c.304C>T · rs199651638 · VCV3099319

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8346 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0156%, eas)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.8346	likely pathogenic
REVEL	0.547	indeterminate
SaProt	LLR -15.06	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 4	GERP 2, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 1,154 bp · p 0.061 · regional, not allelic
Overall
CADD	25.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

Grpmax group 0.0156% East Asian · 7/44,896 alleles

Filtering AF 0.00726% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00514%

Overall 0.000867% 14/1,614,024 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0156%	6,414
Remaining individualsnot grpmax-eligible	0.0032%	31,245
European (non-Finnish)	0.000424%	236,005

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: GDPGP1
Protein: p.Arg102Cys
Coding: c.304C>T
MANE Select: NM_006384 · reported on NM_001013657
dbSNP: rs199651638
Type: single nucleotide variant
Location: chr15:90241212 (GRCh38)

Full GDPGP1 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/gdpgp1-p-arg102cys (accessed [today's date]).

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