DMTF1 p.Ala38=
c.114G>A · rs760468410 · VCV749224
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.033%, mid)
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 1.4 | GERP -1.5, phastCons 1 |
| Overall | ||
| CADD | 19.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.033%
Middle Eastern · 2/6,056 alleles
Filtering AF
0.0103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00816%
Overall
0.00193%
31/1,608,928 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.033% | 3,028 |
| African / African-American | 0.0174% | 5,740 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,152 |
| East Asian | 0.00223% | 44,814 |
| South Asian | 0.00222% | 45,015 |
| European (non-Finnish) | 0.000933% | 107,126 |
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
- DMTF1
- Protein
- p.Ala38=
- Coding
- c.114G>A
- MANE Select
- NM_001142327
- dbSNP
- rs760468410
- Type
- single nucleotide variant
- Location
- chr7:87166487 (GRCh38)
- Gene constraint
- LOEUF 0.539 · pLI 0.72 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 53.56 · 1 PDB
- Residue 38
- the 'interaction with ccnd2' region
Similar variants
- DMTF1 p.Ala38Thr Uncertain significance ★ ⚠ same residue
- DMTF1 p.Ala38Val 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
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/dmtf1-p-ala38 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown