DSPP p.Ser862del
c.2582GTA[1] · rs757110553 · VCV2654896
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.175%, 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 -3.3 | GERP -1 |
| Overall | ||
| CADD | 0.403 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | GATAGCAGT simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.175%
African / African-American · 121/69,224 alleles
Filtering AF
0.149%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.14%
Overall
0.00886%
135/1,524,422 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.175% | 572 |
| Remaining individualsnot grpmax-eligible | 0.0102% | 9,798 |
| Admixed American | 0.0102% | 9,823 |
| South Asian | 0.00123% | 81,206 |
| European (non-Finnish) | 0.000176% | 566,874 |
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.Ser862del
- Coding
- c.2582GTA[1]
- dbSNP
- rs757110553
- Type
- Microsatellite
- Location
- chr4:87615243 (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-ser862del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown