Is UMPS p.Ala302Val (c.905C>T) pathogenic?

UMPS p.Ala302Val (c.905C>T) is classified Uncertain significance in UMPS (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-05). AlphaMissense: ambiguous (0.523); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with UMPS p.Ala302Val (c.905C>T)?

UMPS p.Ala302Val (c.905C>T) is associated with Inborn genetic diseases (ClinVar).

How common is UMPS p.Ala302Val (c.905C>T) in the general population?

UMPS p.Ala302Val (c.905C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about UMPS p.Ala302Val (c.905C>T)?

AlphaMissense predicts ambiguous (score 0.523) — an in-silico prediction, not a clinical call.

UMPS p.Ala302Val

c.905C>T · VCV3977607

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.523 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.523	ambiguous
REVEL	0.581	indeterminate
SaProt	LLR -12.62	damaging
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 7.7	GERP 2.4, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 14 kb · p 0.016 · regional, not allelic
Overall
CADD	27.5	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: UMPS
Protein: p.Ala302Val
Coding: c.905C>T
MANE Select: NM_000373
Type: single nucleotide variant
Location: chr3:124738162 (GRCh38)
Gene constraint: LOEUF 0.735 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.36 · 125 PDB
Residue 302: the 'ompdecase' region; an α-helix

Full UMPS 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

UMPS p.Ala386Val Uncertain significance ★★ ⚠ same condition
UMPS p.Cys72Phe Uncertain significance ★★ ⚠ same condition
UMPS p.Ile318Thr Uncertain significance ★★ ⚠ same condition
UMPS p.Val12Gly Uncertain significance ★★ ⚠ same condition
UMPS p.Leu120= Likely benign ★★ same condition
UMPS p.Ala165Val Uncertain significance ★ ⚠ same condition
UMPS p.Ala208Val Uncertain significance ★ ⚠ same condition
UMPS p.Ala2Val 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/umps-p-ala302val (accessed [today's date]).

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