DNTT p.Gln454=
c.1362G>A · VCV4243695
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.87 | acceptor loss, 1 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.86 | GERP -1.7, phastCons 1 |
| Overall | ||
| CADD | 10.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,890 alleles
Overall
0.000205%
3/1,461,842 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,890 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
| South Asian | 0.0011% | 91,090 |
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.Gln454=
- Coding
- c.1362G>A
- MANE Select
- NM_004088
- Type
- single nucleotide variant
- Location
- chr10:96335893 (GRCh38)
- Gene constraint
- LOEUF 0.942 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.49 · 2 PDB
- Residue 454
- 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.Glu244= Benign/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
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-gln454 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown