DMP1 p.Ser274=
c.822A>G · rs888983238 · VCV2086590
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.6 | GERP -3.3 |
| Overall | ||
| CADD | 0.354 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,024 alleles
Overall
6.84e-05%
1/1,461,826 alleles · very rare
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
- DMP1
- Protein
- p.Ser274=
- Coding
- c.822A>G
- MANE Select
- NM_001142327 · reported on NM_004407
- dbSNP
- rs888983238
- Type
- single nucleotide variant
- Location
- chr4:87662600 (GRCh38)
- Structure
- AlphaFold pLDDT 53.56 · 1 PDB
- Residue 274
- the hth myb-type domain; the 'required for dna-binding' region; the 'interaction with ccnd1, ccnd2 and ccnd3' region
Similar variants
- DMP1 p.Gly135Ter Pathogenic/Likely pathogenic ★★ same type
- DMP1 p.Met1Val Pathogenic/Likely pathogenic ★★ same type
- DMP1 c.*159T>A Uncertain significance ★★ same type
- DMP1 c.*77T>C Uncertain significance ★★ same type
- DMP1 p.Arg173Trp Uncertain significance ★★ ⚠ same type
- DMP1 p.Arg302Ile Uncertain significance ★★ ⚠ same type
- DMP1 p.Arg310Lys Uncertain significance ★★ ⚠ same type
- DMP1 p.Asn233Lys Uncertain significance ★★ ⚠ same type
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/dmp1-p-ser274 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown