DPH1 p.Lys38=
c.114G>A · rs971764185 · VCV3051893
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Conditions
1
DPH1-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 0.23 | GERP -2.2, phastCons 0.97 |
| Overall | ||
| CADD | 6.937 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,084 alleles
Overall
6.84e-05%
1/1,461,868 alleles · very rare
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.Lys38=
- Coding
- c.114G>A
- MANE Select
- NM_001383
- dbSNP
- rs971764185
- Type
- single nucleotide variant
- Location
- chr17:2033557 (GRCh38)
- Gene constraint
- LOEUF 1.321 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.00
Disease context
DPH1-related disorder
Similar variants
- DPH1 p.Lys38Thr Likely benign ★★ same residue
- DPH1 p.Met1Lys Likely pathogenic ★ ⚠ same condition
- DPH1 p.Ser183= Benign same condition
- DPH1 p.Tyr128= Likely benign same condition
- DPH1 p.Val257= Likely benign same condition
- DPH1 p.Leu229Pro Pathogenic/Likely pathogenic ★★ same type
- DPH1 p.Arg144Trp Uncertain significance ★★ ⚠ same type
- DPH1 p.Arg22Gln 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-lys38 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown