DPH1 p.Pro34=
c.102T>G · rs1597275501 · VCV726667
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0234%, 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 1.2 | GERP -0.93, phastCons 1 |
| Overall | ||
| CADD | 9.492 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0234%
European (non-Finnish) · 274/1,173,336 alleles
Filtering AF
0.0211%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0202%
Overall
0.0194%
312/1,606,450 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0234% | 4,282 |
| Middle Eastern | 0.0165% | 6,058 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0135% | 7,388 |
| Remaining individualsnot grpmax-eligible | 0.0129% | 7,779 |
| East Asian | 0.0112% | 8,957 |
| Finnishnot grpmax-eligible | 0.011% | 9,129 |
| South Asian | 0.0088% | 11,367 |
| African / African-American | 0.00535% | 18,690 |
| Admixed American | 0.00167% | 59,974 |
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.Pro34=
- Coding
- c.102T>G
- MANE Select
- NM_001383
- dbSNP
- rs1597275501
- Type
- single nucleotide variant
- Location
- chr17:2033545 (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-pro34 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown