DNTT p.Asn165=
c.495C>T · rs34111381 · VCV709704
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.721%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.22 | donor loss · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP 0.63, phastCons 0.94 |
| Overall | ||
| CADD | 8.868 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.721%
African / African-American · 541/74,988 alleles
Filtering AF
0.671%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.651%
Overall
0.0366%
590/1,613,680 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.721% | 139 |
| Remaining individualsnot grpmax-eligible | 0.056% | 1,785 |
| Admixed American | 0.02% | 5,001 |
| South Asian | 0.0011% | 91,040 |
| European (non-Finnish) | 8.48e-05% | 1,179,696 |
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.Asn165=
- Coding
- c.495C>T
- MANE Select
- NM_004088
- dbSNP
- rs34111381
- Type
- single nucleotide variant
- Location
- chr10:96319378 (GRCh38)
- Gene constraint
- LOEUF 0.942 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.49 · 2 PDB
- Residue 165
- 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-asn165 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown