DYNC2LI1 p.Phe219=
c.657T>C · rs999485995 · VCV2974542
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00408%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.108 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.61 | GERP 0.67, phastCons 1 |
| Overall | ||
| CADD | 8.524 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00408%
African / African-American · 3/73,554 alleles
Filtering AF
0.00108%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0005%
Overall
0.00019%
3/1,577,464 alleles · very rare
exomes 0/1,425,380 · genomes 3/152,084 · 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
- DYNC2LI1
- Protein
- p.Phe219=
- Coding
- c.657T>C
- MANE Select
- NM_016008
- dbSNP
- rs999485995
- Type
- single nucleotide variant
- Location
- chr2:43800843 (GRCh38)
- Gene constraint
- LOEUF 1.028 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.49 · 3 PDB
Similar variants
- DYNC2LI1 p.Leu117Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- DYNC2LI1 p.Trp124Ter Pathogenic/Likely pathogenic ★★ same type
- ABCG5 p.Ala505Asp Uncertain significance ★★ ⚠ same type
- ABCG5 p.Gly288Ser Uncertain significance ★★ ⚠ same type
- ABCG5 p.Ser361Cys Uncertain significance ★★ ⚠ same type
- ABCG5 p.Val420Gly Uncertain significance ★★ ⚠ same type
- DYNC2LI1 p.Cys203Tyr Uncertain significance ★★ same type
- DYNC2LI1 p.Glu23Lys 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/dync2li1-p-phe219 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown