DSPP p.Asp1113=
c.3339T>C · rs373236680 · VCV1217808
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.85%, 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 -2.3 |
| Overall | ||
| CADD | 1.96 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.85%
African / African-American · 214/11,578 alleles
Filtering AF
1.65%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.57%
Overall
0.104%
459/441,222 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.85% | 54 |
| East Asian | 0.214% | 466 |
| Admixed American | 0.199% | 503 |
| Remaining individualsnot grpmax-eligible | 0.188% | 533 |
| South Asian | 0.0951% | 1,051 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0756% | 1,323 |
| Middle Eastern | 0.0519% | 1,928 |
| Finnishnot grpmax-eligible | 0.0344% | 2,903 |
| European (non-Finnish) | 0.0335% | 2,989 |
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.Asp1113=
- Coding
- c.3339T>C
- dbSNP
- rs373236680
- Type
- single nucleotide variant
- Location
- chr4:87616001 (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-asp1113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown