BICD2 p.Lys849Gln
c.2545A>C · rs1412613776 · VCV1497175
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 8.53e-05%, nfe)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.159 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.9 | GERP 2.2, phastCons 1 |
| Regional constraint | o/e 0.72 | unconstrained · MANE · 3,839 bp · p 5.4e-09 · regional, not allelic |
| Overall | ||
| CADD | 25.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.53e-05%
European (non-Finnish) · 1/1,171,936 alleles
Overall
6.9e-05%
1/1,449,368 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.Lys849Gln
- Coding
- c.2545A>C
- MANE Select
- NM_001003800
- dbSNP
- rs1412613776
- Type
- single nucleotide variant
- Location
- chr9:92715177 (GRCh38)
- Gene constraint
- LOEUF 0.507 · pLI 0.95 (gnomAD)
- Structure
- AlphaFold pLDDT 78.89 · 2 PDB
Similar variants
- BICD2 p.Lys849Asn Uncertain significance ★ same residue
- BICD2 p.Arg694Cys Pathogenic/Likely pathogenic ★★ same condition
- BICD2 p.Arg694Gly Pathogenic/Likely pathogenic ★★ same condition
- BICD2 p.Lys734Glu Likely pathogenic ★★ same condition
- BICD2 p.Ser107Leu Pathogenic ★★ ⚠ same condition
- BICD2 p.Thr703Met Pathogenic/Likely pathogenic ★★ same condition
- BICD2 p.Tyr538Cys Pathogenic ★★ ⚠ same condition
- BICD2 p.Tyr556Ser Likely pathogenic ★★ ⚠ same condition
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-lys849gln (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown