DMGDH p.Arg477=
c.1429A>C · rs192307313 · VCV3037136
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.283%, eas)
Conditions
1
DMGDH-related disorder
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 2.8 | GERP -0.075, phastCons 0.28 |
| Overall | ||
| CADD | 6.66 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.283%
East Asian · 127/44,886 alleles
Filtering AF
0.243%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.228%
Overall
0.0162%
262/1,614,210 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.283% | 353 |
| Remaining individualsnot grpmax-eligible | 0.117% | 856 |
| South Asian | 0.0582% | 1,718 |
| Admixed American | 0.00333% | 30,013 |
| African / African-American | 0.00133% | 75,056 |
| European (non-Finnish) | 0.000508% | 196,673 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- DMGDH
- Protein
- p.Arg477=
- Coding
- c.1429A>C
- MANE Select
- NM_013391
- dbSNP
- rs192307313
- Type
- single nucleotide variant
- Location
- chr5:79032775 (GRCh38)
- Gene constraint
- LOEUF 0.942 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.13 · 1 PDB
- Residue 477
- an α-helix
Disease context
DMGDH-related disorder
Similar variants
- DMGDH c.101+10G>T Likely benign same condition
- DMGDH c.1814+10C>T Likely benign same condition
- DMGDH p.Leu105= Likely benign same condition
- DMGDH p.Phe754Ser Benign same condition
- DMGDH p.Pro23= Likely benign same condition
- DMGDH p.Tyr186Cys Likely benign ⚠ same condition
- DMGDH p.His109Arg Likely pathogenic ★★ ⚠ same type
- DMGDH p.Arg719Cys 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/dmgdh-p-arg477 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown