DSPP p.Ser1214=
c.3642C>T · rs111240022 · VCV2654931
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0976%, nfe)
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 -3 |
| Overall | ||
| CADD | 0.06 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0976%
European (non-Finnish) · 963/986,246 alleles
Filtering AF
0.0925%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0904%
Overall
0.0815%
1,082/1,328,192 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0976% | 1,024 |
| Remaining individualsnot grpmax-eligible | 0.0781% | 1,280 |
| Middle Eastern | 0.0779% | 1,283 |
| Admixed American | 0.0626% | 1,597 |
| South Asian | 0.0477% | 2,099 |
| African / African-American | 0.0163% | 6,129 |
| Finnishnot grpmax-eligible | 0.00594% | 16,833 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00401% | 24,954 |
| East Asian | 0.00277% | 36,164 |
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.Ser1214=
- Coding
- c.3642C>T
- dbSNP
- rs111240022
- Type
- single nucleotide variant
- Location
- chr4:87616304 (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-ser1214 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown