BICD2

protein-coding

BICD 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

NM_001003800.2

Inheritance

AD, AR

ClinVar variants

P:43U:409B:402

Top phenotype

Spinal muscular atrophy, lower extremity-predominant, 2A, childhood onset, autosomal dominant; Spinal muscular atrophy, lower extremity-predominant, 2B, prenatal onset, autosomal dominant

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr9:92,711,363-92,764,833

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~53.5 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

autosomal dominant childhood-onset proximal spinal muscular atrophy with contracturesDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0014121

Submitter: G2P

neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

autosomal dominant childhood-onset proximal spinal muscular atrophy with contracturesSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014121

Submitter: Genomics England PanelApp

autosomal dominant childhood-onset proximal spinal muscular atrophy with contracturesSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014121

Submitter: Ambry Genetics

autosomal dominant childhood-onset proximal spinal muscular atrophy with contracturesSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0014121

Submitter: Orphanet

autosomal dominant childhood-onset proximal spinal muscular atrophy with contracturesSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014121

Submitter: PanelApp Australia

spinal muscular atrophy, lower extremity-predominant, 2b, prenatal onset, autosomal dominantSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032660

Submitter: PanelApp Australia

autosomal dominant childhood-onset proximal spinal muscular atrophy with contracturesSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014121

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Spinal muscular atrophy, lower extremity-predominant, 2A, childhood onset, autosomal dominant; Spinal muscular atrophy, lower extremity-predominant, 2B, prenatal onset, autosomal dominantAD

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

Refs: 23664116; 23664119; 23664120; 27751653; 28635954; 30054298Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BICD2 variants in ClinVar

39 Conditions Cataloged
Autosomal dominant childhood-onset proximal spinal muscular atrophy with contracturesTotal: 797
Inborn genetic diseasesTotal: 210
not providedTotal: 186
not specifiedTotal: 96
BICD2-related disorderTotal: 45
Spinal muscular atrophy, lower extremity-predominant, 2b, prenatal onset, autosomal dominantTotal: 17
Neuronopathy, distal hereditary motor, autosomal dominantTotal: 5
Spastic paraplegiaTotal: 3

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
258
clinvar
9
clinvar
271
missense
11
clinvar
30
clinvar
384
clinvar
128
clinvar
7
clinvar
560
nonsense
1
clinvar
1
clinvar
8
clinvar
10
start loss
1
clinvar
1
frameshift
8
clinvar
8
splice donor/acceptor (+/-2bp)
4
clinvar
4
Total123140938616854

Highest pathogenic variant AF is 0.0000013693096

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001003800.2RefSeqNP_001003800.17MANE Select
ENST00000356884.11EnsemblENSP00000349351.67MANE Select
NM_015250.4RefSeqNP_056065.18Standard
ENST00000375512.3EnsemblENSP00000364662.38Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.214145610.7380.00003995544
Missense (PolyPhen)120230.690.520182319
Synonymous-0.4462602511.040.00001801745
Loss of Function4.40430.00.1330.00000137370

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000120.000062rare
Latino/Admixed American0.0000900.000087rare
Ashkenazi Jewish00.0absent
East Asian0.000110.00011rare
Finnish00.0absent
European (Non-Finnish)0.0000460.000044rare
South Asian0.000170.000098rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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