DYNLT2B p.Glu19=
c.57G>A · rs145476537 · VCV779236
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.987%, afr)
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 0.38 | GERP -0.37, phastCons 0.99 |
| Overall | ||
| CADD | 6.035 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.987%
African / African-American · 701/71,022 alleles
Filtering AF
0.926%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.902%
Overall
0.0483%
757/1,567,116 alleles · rare
exomes 353/1,414,942 · genomes 404/152,174 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.987% | 101 |
| Remaining individualsnot grpmax-eligible | 0.0527% | 1,897 |
| Middle Eastern | 0.0336% | 2,975 |
| Admixed American | 0.0295% | 3,394 |
| South Asian | 0.00351% | 28,506 |
| European (non-Finnish) | 0.000258% | 387,238 |
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.Glu19=
- Coding
- c.57G>A
- MANE Select
- NM_152773
- dbSNP
- rs145476537
- Type
- single nucleotide variant
- Location
- chr3:196318096 (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-glu19 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown