DSPP p.Ser1004=
c.3012T>C · VCV3388867
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0029%, 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 -1.6 |
| Overall | ||
| CADD | 0.327 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0029%
African / African-American · 2/68,886 alleles
Filtering AF
0.000482%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00018%
Overall
0.000394%
6/1,524,400 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0029% | 34,443 |
| Finnishnot grpmax-eligible | 0.00173% | 57,648 |
| South Asian | 0.00123% | 81,412 |
| European (non-Finnish) | 0.000176% | 567,379 |
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.Ser1004=
- Coding
- c.3012T>C
- Type
- single nucleotide variant
- Location
- chr4:87615674 (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-ser1004 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown