DYNC2LI1 p.Gln316=
c.948G>A · rs370691743 · VCV2723829
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00925%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.186 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP -2.7, phastCons 1 |
| Overall | ||
| CADD | 4.455 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00925%
European (non-Finnish) · 109/1,178,512 alleles
Filtering AF
0.00783%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00728%
Overall
0.00701%
113/1,612,190 alleles · very rare
exomes 101/1,459,900 · genomes 12/152,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00925% | 10,812 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,213 |
| African / African-American | 0.00133% | 74,986 |
| South Asian | 0.0011% | 90,980 |
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.Gln316=
- Coding
- c.948G>A
- MANE Select
- NM_016008
- dbSNP
- rs370691743
- Type
- single nucleotide variant
- Location
- chr2:43805201 (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-gln316 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown