Is GMPPA p.Ser298= (c.894G>A) pathogenic?

GMPPA p.Ser298= (c.894G>A) is classified Likely benign in GMPPA (ClinVar, Single submitter, 1 submitter; last evaluated 2018-05-08). Ultra-rare (popmax 0.0117%, amr).

How common is GMPPA p.Ser298= (c.894G>A) in the general population?

GMPPA p.Ser298= (c.894G>A) is ultra-rare (popmax 0.0117%, amr) (gnomAD).

GMPPA p.Ser298=

c.894G>A · rs771155229 · VCV682213

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0117%, 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 -9.2	GERP -2.3
Overall
CADD	0.092	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0117% Admixed American · 7/59,868 alleles

Filtering AF 0.00545% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00381%

Overall 0.00143% 23/1,606,890 alleles · ultra-rare exomes 21/1,454,688 · genomes 2/152,202 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0117%	8,553
South Asian	0.00771%	12,974
European (non-Finnish)	0.000764%	130,870

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: GMPPA
Protein: p.Ser298=
Coding: c.894G>A
MANE Select: NM_013335
dbSNP: rs771155229
Type: single nucleotide variant
Location: chr2:219505755 (GRCh38)

Full GMPPA 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/gmppa-p-ser298 (accessed [today's date]).

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