BICD2
protein-codingBICD cargo adaptor 2
Gene summary
This gene is one of two human homologs of Drosophila bicaudal-D and a member of the Bicoid family. It has been implicated in dynein-mediated, minus end-directed motility along microtubules. It has also been reported to be a phosphorylation target of NIMA related kinase 8. Two alternative splice variants have been described. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~53.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0014121
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0700092
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0014121
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0014121
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0014121
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0014121
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0032660
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0014121
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Musculoskeletal; Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to BICD2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001003800.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 258 | 9 | 271 | ||
| missense | 11 | 30 | 384 | 128 | 7 | 560 |
| nonsense | 1 | 1 | 8 | 10 | ||
| start loss | 1 | 1 | ||||
| frameshift | 8 | 8 | ||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 12 | 31 | 409 | 386 | 16 | 854 |
Highest pathogenic variant AF is 0.0000013693096
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001003800.1 | 7 | MANE Select | |
| Ensembl | ENSP00000349351.6 | 7 | MANE Select | |
| RefSeq | NP_056065.1 | 8 | Standard | |
| Ensembl | ENSP00000364662.3 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vesicle-mediated transport
- Membrane Trafficking
- COPI-independent Golgi-to-ER retrograde traffic
- Golgi-to-ER retrograde transport
- Intra-Golgi and retrograde Golgi-to-ER traffic
Biological Process
- retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
- protein transport
- protein localization to Golgi apparatus
- mRNA transport
- centrosome localization
Molecular Function
- protein binding
- cytoskeletal adaptor activity
- Rab GTPase binding
- dynactin binding
- dynein light intermediate chain binding
Cellular Component
- nuclear envelope
- annulate lamellae
- nuclear pore
- cytoplasm
- Golgi apparatus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000356884
- Coding exons
- 7
- Length
- 53450
- Individuals with no LoFs
- 125732
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 14
- Defined
- 125746
- p
- 0.0000557
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.21 | 414 | 561 | 0.738 | 0.0000399 | 5544 |
| Missense (PolyPhen) | 120 | 230.69 | 0.52018 | 2319 | ||
| Synonymous | -0.446 | 260 | 251 | 1.04 | 0.0000180 | 1745 |
| Loss of Function | 4.40 | 4 | 30.0 | 0.133 | 0.00000137 | 370 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.000062 | rare |
| Latino/Admixed American | 0.000090 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000046 | 0.000044 | rare |
| South Asian | 0.00017 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acts as an adapter protein linking the dynein motor complex to various cargos and converts dynein from a non- processive to a highly processive motor in the presence of dynactin. Facilitates and stabilizes the interaction between dynein and dynactin and activates dynein processivity (the ability to move along a microtubule for a long distance without falling off the track) (By similarity). Facilitates the binding of RAB6A to the Golgi by stabilizing its GTP-bound form. Regulates coat complex coatomer protein I (COPI)-independent Golgi-endoplasmic reticulum transport via its interaction with RAB6A and recruitment of the dynein-dynactin motor complex (PubMed:25962623). Contributes to nuclear and centrosomal positioning prior to mitotic entry through regulation of both dynein and kinesin-1. During G2 phase of the cell cycle, associates with RANBP2 at the nuclear pores and recruits dynein and dynactin to the nuclear envelope to ensure proper positioning of the nucleus relative to centrosomes prior to the onset of mitosis (By similarity). {ECO:0000250|UniProtKB:Q921C5, ECO:0000269|PubMed:25962623}.;
- Disease
- DISEASE: Spinal muscular atrophy, lower extremity-predominant 2, autosomal dominant (SMALED2) [MIM:615290]: An autosomal dominant form of spinal muscular atrophy characterized by early-childhood onset of muscle weakness and atrophy predominantly affecting the proximal and distal muscles of the lower extremity, although some patients may show upper extremity involvement. The disorder results in delayed walking, waddling gait, difficulty walking, and loss of distal reflexes. Some patients may have foot deformities or hyperlordosis, and some show mild upper motor signs, such as spasticity. Sensation, bulbar function, and cognitive function are preserved. The disorder shows very slow progression throughout life. {ECO:0000269|PubMed:23664116, ECO:0000269|PubMed:23664119, ECO:0000269|PubMed:23664120}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- LoFtool
- 0.468
- RVIS EVS
- -1.39
- RVIS percentile EVS
- 4.25
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.918
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |