DSPP p.Gly442=
c.1326T>C · rs117746821 · VCV1286988
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.64%, eas)
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 -4.2 | GERP -2.8 |
| Overall | ||
| CADD | 1.232 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.64%
East Asian · 1,635/44,876 alleles
Filtering AF
3.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.44%
Overall
0.114%
1,834/1,614,156 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 3.64% | 27 |
| Remaining individualsnot grpmax-eligible | 0.245% | 409 |
| South Asian | 0.0187% | 5,358 |
| Admixed American | 0.0117% | 8,575 |
| African / African-American | 0.00533% | 18,756 |
| European (non-Finnish) | 0.00153% | 65,557 |
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.Gly442=
- Coding
- c.1326T>C
- dbSNP
- rs117746821
- Type
- single nucleotide variant
- Location
- chr4:87613988 (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-gly442 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown