Is DPM3 p.Thr63Ser (c.187A>T) pathogenic?

DPM3 p.Thr63Ser (c.187A>T) is classified Uncertain significance in DPM3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-21). AlphaMissense: likely benign (0.1643); Absent from gnomAD v4.1.

How common is DPM3 p.Thr63Ser (c.187A>T) in the general population?

DPM3 p.Thr63Ser (c.187A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DPM3 p.Thr63Ser (c.187A>T)?

AlphaMissense predicts likely benign (score 0.1643) — an in-silico prediction, not a clinical call.

DPM3 p.Thr63Ser

c.187A>T · rs2526668194 · VCV3085505

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1643 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1643	likely benign
REVEL	0.671	pathogenic-leaning
SaProt	LLR -11.20	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 1.6, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 275 bp · p 0.45 · regional, not allelic
Overall
CADD	24.8	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: DPM3
Protein: p.Thr63Ser
Coding: c.187A>T
MANE Select: NM_153741
dbSNP: rs2526668194
Type: single nucleotide variant
Location: chr1:155140054 (GRCh38)
Gene constraint: LOEUF 1.364 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 88.73

Full DPM3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DPM3 p.Thr63Ala Uncertain significance ★ same residue
DPM3 p.Ala70Thr Uncertain significance ★★ ⚠ same type
DPM3 p.Ala86Asp Uncertain significance ★★ ⚠ same type
DPM3 p.Arg60Cys Uncertain significance ★★ ⚠ same type
DPM3 p.Arg60Leu Uncertain significance ★★ ⚠ same type
DPM3 p.Gln6His Uncertain significance ★★ ⚠ same type
DPM3 p.Glu73Ala Uncertain significance ★★ ⚠ same type
DPM3 p.Gly50Ser Uncertain significance ★★ ⚠ same type

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/dpm3-p-thr63ser (accessed [today's date]).

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