DPH1 p.Ser414=
c.1242C>T · rs573588613 · VCV750630
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.201%, 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 -0.22 | GERP -3.2 |
| Overall | ||
| CADD | 9.481 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.201%
South Asian · 181/89,936 alleles
Filtering AF
0.177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.168%
Overall
0.0124%
199/1,605,544 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.201% | 497 |
| Remaining individualsnot grpmax-eligible | 0.0113% | 8,867 |
| European (non-Finnish) | 0.000935% | 106,972 |
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.Ser414=
- Coding
- c.1242C>T
- MANE Select
- NM_001383
- dbSNP
- rs573588613
- Type
- single nucleotide variant
- Location
- chr17:2041782 (GRCh38)
- Gene constraint
- LOEUF 1.321 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.00
- Residue 414
- the 'disordered' region
Similar variants
- DPH1 p.Ser414Ala 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-ser414 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown