DHPS p.Asn175=
c.525T>C · rs1208117313 · VCV2649342
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 1.6 | GERP 0.53, phastCons 1 |
| Overall | ||
| CADD | 7.652 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.000247%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000159%
Overall
0.000496%
8/1,614,086 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| European (non-Finnish) | 0.000593% | 168,578 |
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
- DHPS
- Protein
- p.Asn175=
- Coding
- c.525T>C
- MANE Select
- NM_001930
- dbSNP
- rs1208117313
- Type
- single nucleotide variant
- Location
- chr19:12679689 (GRCh38)
- Gene constraint
- LOEUF 0.824 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.95 · 89 PDB
- Residue 175
- an α-helix
Similar variants
- DHPS p.Glu71Lys Uncertain significance ★★ ⚠ same type
- DHPS p.Gly162Arg Uncertain significance ★★ ⚠ same type
- DHPS p.Met124Leu Uncertain significance ★★ ⚠ same type
- DHPS c.784+8G>T Likely benign ★★ same type
- DHPS p.Lys358= Likely benign ★★ same type
- DHPS p.Thr88= Likely benign ★★ same type
- DHPS c.785-1G>C Likely pathogenic ★ same type
- DHPS p.Gln194Ter Likely pathogenic ★ 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/dhps-p-asn175 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown