Is DPM1 p.Arg234= (c.702T>C) pathogenic?

DPM1 p.Arg234= (c.702T>C) is classified Likely benign in DPM1 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-04-14). Absent from gnomAD v4.1; Associated with congenital disorder of glycosylation type 1E.

What condition is associated with DPM1 p.Arg234= (c.702T>C)?

DPM1 p.Arg234= (c.702T>C) is associated with congenital disorder of glycosylation type 1E (ClinVar).

How common is DPM1 p.Arg234= (c.702T>C) in the general population?

DPM1 p.Arg234= (c.702T>C) is absent from gnomAD v4.1 (gnomAD).

How is DPM1-CDG inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

DPM1 p.Arg234=

c.702T>C · rs2123056796 · VCV1123790

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

congenital disorder of glycosylation type 1E

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.042	moderately benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.19	GERP -2.9, phastCons 0.6
Overall
CADD	5.906	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: DPM1
Protein: p.Arg234=
Coding: c.702T>C
dbSNP: rs2123056796
Type: single nucleotide variant
Location: chr20:50935213 (GRCh38)

Full DPM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

congenital disorder of glycosylation type 1E — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For DPM1-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

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/dpm1-p-arg234 (accessed [today's date]).

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