DPH1 p.Ala194=
c.582C>T · rs187964662 · VCV740425
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0333%, afr)
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 -0.34 | GERP -3.4, phastCons 0.36 |
| Overall | ||
| CADD | 10.86 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0333%
African / African-American · 25/75,014 alleles
Filtering AF
0.0231%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0197%
Overall
0.00347%
56/1,613,612 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0333% | 3,001 |
| Admixed American | 0.0133% | 7,500 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,832 |
| East Asian | 0.00223% | 44,874 |
| South Asian | 0.0022% | 45,534 |
| Finnishnot grpmax-eligible | 0.00157% | 63,632 |
| European (non-Finnish) | 0.00136% | 73,747 |
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
- DPH1
- Protein
- p.Ala194=
- Coding
- c.582C>T
- MANE Select
- NM_001383
- dbSNP
- rs187964662
- Type
- single nucleotide variant
- Location
- chr17:2036858 (GRCh38)
- Gene constraint
- LOEUF 1.321 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.00
Similar variants
- OVCA2 p.Phe194Ser Uncertain significance ★ ⚠ same residue
- DPH1 p.Leu229Pro Pathogenic/Likely pathogenic ★★ same type
- DPH1 p.Arg144Trp Uncertain significance ★★ ⚠ same type
- DPH1 p.Arg22Gln Uncertain significance ★★ ⚠ same type
- DPH1 p.Arg27His Uncertain significance ★★ ⚠ same type
- DPH1 p.Arg47Trp Uncertain significance ★★ ⚠ same type
- DPH1 p.Asp231Glu Uncertain significance ★★ ⚠ same type
- DPH1 p.Gln269His 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/dph1-p-ala194 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown