DMP1 p.Phe9=
c.27C>T · VCV4773718
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00892%, eas)
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 0.62 | GERP -1, phastCons 0.002 |
| Overall | ||
| CADD | 4.586 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00892%
East Asian · 4/44,838 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0018%
Overall
0.000343%
5/1,457,866 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00892% | 11,210 |
| European (non-Finnish) | 8.5e-05% | 1,176,430 |
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.Phe9=
- Coding
- c.27C>T
- MANE Select
- NM_001142327 · reported on NM_004407
- Type
- single nucleotide variant
- Location
- chr4:87656519 (GRCh38)
- Structure
- AlphaFold pLDDT 53.56 · 1 PDB
- Residue 9
- the 'interaction with ccnd2' region
Similar variants
- DMP1 p.Phe9Leu Uncertain significance ★ ⚠ same residue
- 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
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-phe9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown