DPM1 p.Ser7=
c.21T>C · VCV4700207
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
congenital disorder of glycosylation type 1E
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.125 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -3.1 |
| Overall | ||
| CADD | 1.521 | 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.Ser7=
- Coding
- c.21T>C
- MANE Select
- NM_003859
- Type
- single nucleotide variant
- Location
- chr20:50958503 (GRCh38)
- Gene constraint
- LOEUF 1.005 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 88.61
Disease context
congenital disorder of glycosylation type 1E — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor DPM1-CDG (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- DPM1 p.Ser7Asn Uncertain significance ★★ ⚠ same residue
- DPM1 p.Ser7Gly Uncertain significance ★★ ⚠ same residue
- DPM1 p.Arg92Gly Pathogenic ★★ same condition
- DPM1 p.His124Arg Likely pathogenic ★★ same condition
- DPM1 p.Met1Leu Pathogenic/Likely pathogenic ★★ same condition
- DPM1 c.*12T>C Uncertain significance ★★ same condition
- DPM1 p.Ala109Val Uncertain significance ★★ ⚠ same condition
- DPM1 p.Arg12Met 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/dpm1-p-ser7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown