Is DPM3 p.Leu74= (c.220C>T) pathogenic?

DPM3 p.Leu74= (c.220C>T) is classified Likely benign in DPM3 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-31). Absent from gnomAD v4.1.

How common is DPM3 p.Leu74= (c.220C>T) in the general population?

DPM3 p.Leu74= (c.220C>T) is absent from gnomAD v4.1 (gnomAD).

DPM3 p.Leu74=

c.220C>T · rs1571703051 · VCV758385

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.4	GERP 0.61, phastCons 1
Overall
CADD	11.41	PHRED · no single calibrated threshold — expert panels disagree

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.Leu74=
Coding: c.220C>T
MANE Select: NM_153741
dbSNP: rs1571703051
Type: single nucleotide variant
Location: chr1:155140021 (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.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
DPM3 p.Gly89Glu 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-leu74 (accessed [today's date]).

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