DYNLT2B p.Val105=
c.315A>G · rs1420454901 · VCV2964250
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.01%, amr)
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 -0.029 | GERP -4.9, phastCons 0.89 |
| Overall | ||
| CADD | 8.604 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/60,014 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.000372%
6/1,613,596 alleles · very rare
exomes 6/1,461,258 · genomes 0/152,338 · 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.Val105=
- Coding
- c.315A>G
- MANE Select
- NM_152773
- dbSNP
- rs1420454901
- Type
- single nucleotide variant
- Location
- chr3:196306945 (GRCh38)
- Gene constraint
- LOEUF 1.236 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.89 · 2 PDB
- Residue 105
- a UniProt-annotated variant site (in srtd17); a β-strand
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-val105 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown