DPH1 p.Ala242=
c.726C>T · rs368555983 · VCV788744
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.103%, nfe)
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 2.2 | GERP 0.15, phastCons 1 |
| Overall | ||
| CADD | 11.88 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.103%
European (non-Finnish) · 1,214/1,180,032 alleles
Filtering AF
0.0981%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0961%
Overall
0.0851%
1,374/1,614,170 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.103% | 972 |
| Middle Eastern | 0.066% | 1,516 |
| South Asian | 0.0604% | 1,656 |
| Remaining individualsnot grpmax-eligible | 0.0592% | 1,689 |
| Admixed American | 0.0466% | 2,144 |
| Finnishnot grpmax-eligible | 0.0266% | 3,764 |
| African / African-American | 0.0253% | 3,951 |
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.Ala242=
- Coding
- c.726C>T
- MANE Select
- NM_001383
- dbSNP
- rs368555983
- Type
- single nucleotide variant
- Location
- chr17:2039800 (GRCh38)
- Gene constraint
- LOEUF 1.321 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.00
Similar variants
- 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
- DPH1 p.Ile241Phe 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-ala242 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown