DMGDH p.Pro493=
c.1479G>A · rs762477431 · VCV384238
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 -1.2 | GERP -2.4, phastCons 0.002 |
| Overall | ||
| CADD | 10.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,894 alleles
Filtering AF
0.0013%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00108%
Overall
0.00167%
27/1,614,048 alleles · very rare
exomes 26/1,461,874 · genomes 1/152,174 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,894 |
| European (non-Finnish) | 0.00195% | 51,307 |
| Admixed American | 0.00167% | 60,000 |
| African / African-American | 0.00133% | 74,908 |
| South Asian | 0.0011% | 91,088 |
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.Pro493=
- Coding
- c.1479G>A
- MANE Select
- NM_013391
- dbSNP
- rs762477431
- Type
- single nucleotide variant
- Location
- chr5:79032725 (GRCh38)
- Gene constraint
- LOEUF 0.942 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.13 · 1 PDB
- Residue 493
- a β-strand
Similar variants
- DMGDH p.His109Arg Likely pathogenic ★★ ⚠ same type
- DMGDH p.Arg719Cys Uncertain significance ★★ ⚠ same type
- DMGDH c.101+143A>T Likely benign ★★ same type
- DMGDH c.102-4C>T Likely benign ★★ same type
- DMGDH c.1518-4T>A Benign/Likely benign ★★ same type
- DMGDH c.1684-22A>G Benign/Likely benign ★★ same type
- DMGDH c.1815-9A>G Benign ★★ same type
- DMGDH c.2250+135T>C Likely benign ★★ 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-pro493 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown