DSPP p.Ser1052=
c.3156T>C · rs368829445 · VCV2654903
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.07%, mid)
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 -13 | GERP -1.8 |
| Overall | ||
| CADD | 1.028 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.07%
Middle Eastern · 4/5,714 alleles
Filtering AF
0.0383%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0332%
Overall
0.00469%
71/1,513,218 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.07% | 1,429 |
| African / African-American | 0.0533% | 1,877 |
| Admixed American | 0.0267% | 3,742 |
| East Asian | 0.0204% | 4,902 |
| Remaining individualsnot grpmax-eligible | 0.0119% | 8,382 |
| Finnishnot grpmax-eligible | 0.00347% | 28,809 |
| South Asian | 0.00243% | 41,146 |
| European (non-Finnish) | 0.00044% | 227,176 |
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.Ser1052=
- Coding
- c.3156T>C
- dbSNP
- rs368829445
- Type
- single nucleotide variant
- Location
- chr4:87615818 (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-ser1052 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown