DMP1 p.Asp206=
c.618C>T · rs369898414 · VCV2889371
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0453%, afr)
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 -8.2 | GERP -2.7 |
| Overall | ||
| CADD | 0.838 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0453%
African / African-American · 34/75,010 alleles
Filtering AF
0.0333%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0292%
Overall
0.00477%
77/1,614,086 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0453% | 2,206 |
| Admixed American | 0.005% | 20,006 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,254 |
| European (non-Finnish) | 0.00297% | 33,715 |
| East Asian | 0.00223% | 44,870 |
| South Asian | 0.0011% | 91,084 |
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.Asp206=
- Coding
- c.618C>T
- MANE Select
- NM_001142327 · reported on NM_004407
- dbSNP
- rs369898414
- Type
- single nucleotide variant
- Location
- chr4:87662396 (GRCh38)
- Structure
- AlphaFold pLDDT 53.56 · 1 PDB
- Residue 206
- the 'interaction with ccnd2' region; 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-asp206 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown