DMP1 p.Gly99del
c.293GAG[1] · rs576066727 · VCV1049127
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.626%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.063 | GERP -2.4 |
| Overall | ||
| CADD | 2.799 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (GAAGAT)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.626%
South Asian · 570/91,092 alleles
Filtering AF
0.583%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.566%
Overall
0.0409%
660/1,614,226 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.626% | 160 |
| Remaining individualsnot grpmax-eligible | 0.0304% | 3,290 |
| Middle Eastern | 0.0165% | 6,062 |
| European (non-Finnish) | 0.00559% | 17,879 |
| African / African-American | 0.004% | 25,022 |
| Admixed American | 0.00167% | 60,022 |
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.Gly99del
- Coding
- c.293GAG[1]
- MANE Select
- NM_001142327 · reported on NM_004407
- dbSNP
- rs576066727
- Type
- Microsatellite
- Location
- chr4:87662069 (GRCh38)
- Structure
- AlphaFold pLDDT 53.56 · 1 PDB
- Residue 99
- the 'interaction with ccnd2' region; the 'required for dna-binding' region; the 'required for transcriptional activation' region
Similar variants
- DMTF1 p.Glu99Gln Uncertain significance ★ ⚠ same residue
- DMTF1 p.Glu99Lys Uncertain significance ★ ⚠ same residue
- DMP1 c.103-17_103-14del Likely benign ★ 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-gly99del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown