DSPP p.Ser836del
c.2504GCA[1] · rs143008261 · VCV804764
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 13.5%, nfe) — too common for a highly-penetrant pathogenic allele
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 -15 | GERP -1.2 |
| Overall | ||
| CADD | 1.965 | 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
13.5%
European (non-Finnish) · 154,722/1,145,906 alleles
Filtering AF
13.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 13.4%
Overall
12%
185,189/1,542,020 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 13.5% | 7 |
| Remaining individualsnot grpmax-eligible | 10.8% | 9 |
| Amishnot grpmax-eligible | 9.79% | 10 |
| Finnishnot grpmax-eligible | 9.69% | 10 |
| Middle Eastern | 9.03% | 11 |
| Ashkenazi Jewishnot grpmax-eligible | 8.75% | 11 |
| Admixed American | 7.95% | 13 |
| East Asian | 5.92% | 17 |
| South Asian | 5.85% | 17 |
| African / African-American | 5.69% | 18 |
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.Ser836del
- Coding
- c.2504GCA[1]
- dbSNP
- rs143008261
- Type
- Microsatellite
- Location
- chr4:87615165 (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-ser836del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown