BICD2 p.Leu311=
c.931C>T · VCV4688342
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
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 -0.033 | GERP -4.8, phastCons 0.007 |
| Overall | ||
| CADD | 2.528 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,044 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000137%
2/1,461,864 alleles · very rare
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
- BICD2
- Protein
- p.Leu311=
- Coding
- c.931C>T
- MANE Select
- NM_001003800
- Type
- single nucleotide variant
- Location
- chr9:92720431 (GRCh38)
- Gene constraint
- LOEUF 0.507 · pLI 0.95 (gnomAD)
- Structure
- AlphaFold pLDDT 78.89 · 2 PDB
- Residue 311
- the 'interacts with dynll1, dync1h1, dync1i2, dctn1 and dctn2' region; the 'disordered' region
Similar variants
- BICD2 p.Leu311Val Uncertain significance ★ ⚠ same residue
- BICD2 p.Arg694Cys Pathogenic/Likely pathogenic ★★ same type
- BICD2 p.Arg694Gly Pathogenic/Likely pathogenic ★★ same type
- BICD2 p.Arg694His Pathogenic/Likely pathogenic ★★ same type
- BICD2 p.Glu774Lys Pathogenic/Likely pathogenic ★★ same type
- BICD2 p.Lys734Glu Likely pathogenic ★★ same type
- BICD2 p.Ser107Leu Pathogenic ★★ ⚠ same type
- BICD2 p.Thr703Met Pathogenic/Likely pathogenic ★★ 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/bicd2-p-leu311 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown