DSPP p.Ser989=
c.2967T>C · VCV3388472
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00685%, 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 -0.79 | GERP -1.8 |
| Overall | ||
| CADD | 0.187 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00685%
African / African-American · 4/58,356 alleles
Filtering AF
0.0023%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00138%
Overall
0.00112%
17/1,511,784 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00685% | 14,589 |
| Admixed American | 0.00207% | 48,344 |
| Finnishnot grpmax-eligible | 0.00174% | 57,546 |
| Remaining individualsnot grpmax-eligible | 0.00172% | 58,294 |
| European (non-Finnish) | 0.000882% | 113,354 |
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.Ser989=
- Coding
- c.2967T>C
- Type
- single nucleotide variant
- Location
- chr4:87615629 (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-ser989 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown