DSPP p.Ser1187=
c.3561T>C · rs369987019 · VCV811560
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.1%, 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 -1.1 |
| Overall | ||
| CADD | 0.228 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.1%
African / African-American · 2,136/68,894 alleles
Filtering AF
2.99%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.95%
Overall
0.327%
4,999/1,530,764 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.1% | 32 |
| Middle Eastern | 2.15% | 47 |
| South Asian | 0.733% | 136 |
| Remaining individualsnot grpmax-eligible | 0.554% | 181 |
| Admixed American | 0.455% | 220 |
| Ashkenazi Jewishnot grpmax-eligible | 0.369% | 271 |
| European (non-Finnish) | 0.125% | 802 |
| East Asian | 0.0799% | 1,252 |
| Finnishnot grpmax-eligible | 0.0466% | 2,146 |
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.Ser1187=
- Coding
- c.3561T>C
- dbSNP
- rs369987019
- Type
- single nucleotide variant
- Location
- chr4:87616223 (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-ser1187 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown