DSPP p.Ser1142=
c.3426T>C · VCV4681277
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.249%, amr)
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 -1.5 |
| Overall | ||
| CADD | 0.719 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.249%
Admixed American · 110/44,192 alleles
Filtering AF
0.211%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.197%
Overall
0.0672%
980/1,458,280 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.249% | 402 |
| East Asian | 0.21% | 475 |
| South Asian | 0.199% | 502 |
| Finnishnot grpmax-eligible | 0.0983% | 1,018 |
| Remaining individualsnot grpmax-eligible | 0.0731% | 1,368 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0602% | 1,661 |
| European (non-Finnish) | 0.0462% | 2,164 |
| African / African-American | 0.0432% | 2,316 |
| Middle Eastern | 0.0386% | 2,593 |
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.Ser1142=
- Coding
- c.3426T>C
- Type
- single nucleotide variant
- Location
- chr4:87616088 (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-ser1142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown