DSPP p.Ser1067=
c.3201T>C · rs777438479 · VCV3025719
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0303%, sas)
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 -2.1 |
| Overall | ||
| CADD | 0.335 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0303%
South Asian · 25/82,452 alleles
Filtering AF
0.021%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.018%
Overall
0.00575%
88/1,529,888 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0303% | 3,298 |
| East Asian | 0.0252% | 3,973 |
| Middle Eastern | 0.0172% | 5,830 |
| Finnishnot grpmax-eligible | 0.0104% | 9,652 |
| Admixed American | 0.0101% | 9,859 |
| African / African-American | 0.0075% | 13,328 |
| Remaining individualsnot grpmax-eligible | 0.00504% | 19,859 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00353% | 28,292 |
| European (non-Finnish) | 0.00281% | 35,604 |
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.Ser1067=
- Coding
- c.3201T>C
- dbSNP
- rs777438479
- Type
- single nucleotide variant
- Location
- chr4:87615863 (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-ser1067 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown