DSPP p.Ser669del
c.2002AGT[1] · rs745344342 · VCV504130
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0508%, 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 0.85 | GERP 1 |
| Overall | ||
| CADD | 1.015 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (CAGTGA)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0508%
African / African-American · 37/72,866 alleles
Filtering AF
0.0378%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0334%
Overall
0.00403%
62/1,538,682 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0508% | 1,969 |
| Middle Eastern | 0.0335% | 2,988 |
| Admixed American | 0.00994% | 10,065 |
| Remaining individualsnot grpmax-eligible | 0.00504% | 19,846 |
| South Asian | 0.0024% | 41,668 |
| Finnishnot grpmax-eligible | 0.00168% | 59,378 |
| European (non-Finnish) | 0.00106% | 94,777 |
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.Ser669del
- Coding
- c.2002AGT[1]
- dbSNP
- rs745344342
- Type
- Microsatellite
- Location
- chr4:87614663 (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-ser669del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown