DMGDH p.Pro467=
c.1401G>A · rs534488827 · VCV507998
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00549%, sas)
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 -5.5 | GERP -4.4 |
| Overall | ||
| CADD | 0.743 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00549%
South Asian · 5/91,062 alleles
Filtering AF
0.0021%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00175%
Overall
0.00266%
43/1,614,120 alleles · very rare
exomes 38/1,461,866 · genomes 5/152,254 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00549% | 18,212 |
| African / African-American | 0.004% | 25,008 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| European (non-Finnish) | 0.0028% | 35,759 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,502 |
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.Pro467=
- Coding
- c.1401G>A
- MANE Select
- NM_013391
- dbSNP
- rs534488827
- Type
- single nucleotide variant
- Location
- chr5:79032803 (GRCh38)
- Gene constraint
- LOEUF 0.942 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.13 · 1 PDB
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-pro467 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown