DSPP p.Ser1163=
c.3489C>T · VCV3898074
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0553%, amr)
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 -1.9 |
| Overall | ||
| CADD | 0.753 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0553%
Admixed American · 15/27,120 alleles
Filtering AF
0.034%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0275%
Overall
0.0148%
142/960,228 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0553% | 1,808 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0538% | 1,860 |
| Finnishnot grpmax-eligible | 0.0378% | 2,645 |
| Middle Eastern | 0.0329% | 3,038 |
| African / African-American | 0.0278% | 3,603 |
| Remaining individualsnot grpmax-eligible | 0.0157% | 6,353 |
| East Asian | 0.0152% | 6,566 |
| European (non-Finnish) | 0.0105% | 9,522 |
| South Asian | 0.00985% | 10,155 |
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.Ser1163=
- Coding
- c.3489C>T
- Type
- single nucleotide variant
- Location
- chr4:87616151 (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-ser1163 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown