DMP1 p.Ser389=
c.1167G>A · rs756632847 · VCV2173051
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0156%, 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 1.1 | GERP -1.3 |
| Overall | ||
| CADD | 3.634 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0156%
East Asian · 7/44,878 alleles
Filtering AF
0.00726%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00515%
Overall
0.0026%
42/1,614,012 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0156% | 6,411 |
| Finnishnot grpmax-eligible | 0.0125% | 8,004 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,242 |
| European (non-Finnish) | 0.00203% | 49,168 |
| African / African-American | 0.00134% | 74,904 |
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.Ser389=
- Coding
- c.1167G>A
- MANE Select
- NM_004407
- dbSNP
- rs756632847
- Type
- single nucleotide variant
- Location
- chr4:87662945 (GRCh38)
- Gene constraint
- LOEUF 1.209 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 47.80
- Residue 389
- the 'disordered' 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-ser389 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown