DSPP p.Ser953=
c.2859T>C · rs772482317 · VCV197808
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0238%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not looked up on this page · why |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -1.5 |
| Overall | ||
| CADD | 0.864 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0238%
African / African-American · 14/58,920 alleles
Filtering AF
0.0143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0114%
Overall
0.00405%
59/1,458,134 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0238% | 4,209 |
| Admixed American | 0.0224% | 4,469 |
| Finnishnot grpmax-eligible | 0.0111% | 9,014 |
| East Asian | 0.00546% | 18,307 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00384% | 26,042 |
| European (non-Finnish) | 0.00218% | 45,820 |
| Remaining individualsnot grpmax-eligible | 0.00178% | 56,088 |
| South Asian | 0.00132% | 75,830 |
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
- DSPP
- Protein
- p.Ser953=
- Coding
- c.2859T>C
- dbSNP
- rs772482317
- Type
- single nucleotide variant
- Location
- chr4:87615521 (GRCh38)
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/dspp-p-ser953 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown