DNTT p.Glu244=
c.732A>G · rs144787508 · VCV780050
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.6%, 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 -1.4, phastCons 1 |
| Overall | ||
| CADD | 5.381 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.6%
Middle Eastern · 96/6,008 alleles
Filtering AF
1.34%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.24%
Overall
0.606%
9,704/1,600,046 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.6% | 63 |
| South Asian | 0.943% | 106 |
| European (non-Finnish) | 0.667% | 150 |
| Remaining individualsnot grpmax-eligible | 0.562% | 178 |
| Finnishnot grpmax-eligible | 0.478% | 209 |
| Amishnot grpmax-eligible | 0.439% | 228 |
| Admixed American | 0.289% | 346 |
| Ashkenazi Jewishnot grpmax-eligible | 0.235% | 426 |
| African / African-American | 0.0802% | 1,248 |
| East Asian | 0.00225% | 44,462 |
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
- DNTT
- Protein
- p.Glu244=
- Coding
- c.732A>G
- MANE Select
- NM_004088
- dbSNP
- rs144787508
- Type
- single nucleotide variant
- Location
- chr10:96322710 (GRCh38)
- Gene constraint
- LOEUF 0.942 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.49 · 2 PDB
- Residue 244
- the 'mediates interaction with dnttip2' region
Similar variants
- DNTT c.203+7C>G Benign ★★ same type
- DNTT c.203+9G>A Benign ★★ same type
- DNTT p.Ala90Val Benign ★★ same type
- DNTT p.Asp280His Likely benign ★★ ⚠ same type
- DNTT p.Ala194Val Uncertain significance ★ ⚠ same type
- DNTT p.Ala195Thr Uncertain significance ★ ⚠ same type
- DNTT p.Ala21Val Uncertain significance ★ ⚠ same type
- DNTT p.Ala239Ser 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/dntt-p-glu244 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown