DYNLT2B p.Ala59=
c.177T>C · VCV3626081
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000339%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.52 | GERP -3.1 |
| Overall | ||
| CADD | 3.775 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000339%
European (non-Finnish) · 4/1,179,946 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000248%
4/1,614,006 alleles · very rare
exomes 4/1,461,674 · genomes 0/152,332 · joint denominator
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
- DYNLT2B
- Protein
- p.Ala59=
- Coding
- c.177T>C
- MANE Select
- NM_152773
- Type
- single nucleotide variant
- Location
- chr3:196316168 (GRCh38)
- Gene constraint
- LOEUF 1.236 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.89 · 2 PDB
Similar variants
- DYNLT2B p.Arg88Ter Pathogenic/Likely pathogenic ★★ same type
- DYNLT2B p.Arg110His Uncertain significance ★★ same type
- DYNLT2B p.Asn119Ser Uncertain significance ★★ ⚠ same type
- DYNLT2B p.Gly6Arg Uncertain significance ★★ ⚠ same type
- DYNLT2B p.Gly6Val Uncertain significance ★★ ⚠ same type
- DYNLT2B p.Ser4Thr Uncertain significance ★★ ⚠ same type
- DYNLT2B p.Val95Leu Uncertain significance ★★ ⚠ same type
- DYNLT2B c.113+17C>G 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/dynlt2b-p-ala59 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown