DSPP p.Ser1115=
c.3345T>C · rs757871880 · VCV1203901
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.69%, eas)
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 -2.4 |
| Overall | ||
| CADD | 1.281 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.69%
East Asian · 639/13,616 alleles
Filtering AF
4.39%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.27%
Overall
1.69%
9,646/571,482 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 4.69% | 21 |
| Finnishnot grpmax-eligible | 3.13% | 32 |
| Remaining individualsnot grpmax-eligible | 1.94% | 51 |
| European (non-Finnish) | 1.63% | 61 |
| Admixed American | 1.36% | 74 |
| African / African-American | 1.21% | 83 |
| South Asian | 1.12% | 89 |
| Ashkenazi Jewishnot grpmax-eligible | 1.01% | 99 |
| Middle Eastern | 0.754% | 133 |
| Amishnot grpmax-eligible | 0.641% | 156 |
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.Ser1115=
- Coding
- c.3345T>C
- dbSNP
- rs757871880
- Type
- single nucleotide variant
- Location
- chr4:87616007 (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-ser1115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown