BICD1

protein-coding

BICD cargo adaptor 1

Gene summary

This gene encodes an adaptor protein that belongs to the bicaudal D family of dynein cargo adaptors. The encoded protein acts as an intracellular cargo transport cofactor that regulates the microtubule-based loading of cargo onto the dynein motor complex. It also controls dynein motor activity and coordination. It has a domain architecture consisting of coiled-coil domains at the N- and C-termini that are highly conserved in other family members. Naturally occurring mutations in this gene are associated with short telomere length and emphysema. [provided by RefSeq, Aug 2017]

MANE transcript

NM_001714.4

Inheritance

—

ClinVar variants

U:113B:6

Top phenotype

BICD1-related condition

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr12:32,106,835-32,383,633

External References & Databases

Ensembl (ENSG00000151746)

Transcript & Mutation Effects

hg38 • Region Span ~276.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BICD1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 110

BICD1-related conditionTotal: 4

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001714.4. 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			1 clinvar	2 clinvar	2 clinvar	5
missense			110 clinvar	2 clinvar		112
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	113	4	2	119

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001714.4	RefSeq	NP_001705.2	10	MANE Select
ENST00000652176.1	Ensembl	ENSP00000498700.1	10	MANE Select
NM_001003398.3	RefSeq	NP_001003398.1	8	Standard
NM_001354186.2	RefSeq	NP_001341115.1	11	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

RNA processing
intracellular mRNA localization
anatomical structure morphogenesis
viral process
protein localization to organelle

Molecular Function

structural constituent of cytoskeleton
protein binding
cytoskeletal adaptor activity
Rab GTPase binding
protein kinase binding

Cellular Component

Golgi apparatus
trans-Golgi network
centrosome
cytosol
cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000281474
Coding exons: 10
Length: 276799
Individuals with no LoFs: 125706
Homozygous LoFs: 0
Heterozygous LoFs: 42
Defined: 125748
p: 0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.27	397	546	0.727	0.0000309	6393
Missense (PolyPhen)		140	244.34	0.57297		2967
Synonymous	0.725	207	221	0.938	0.0000125	1873
Loss of Function	3.77	16	42.5	0.376	0.00000235	526

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00052	0.00043	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.000066	0.000065	rare
Other	0.00036	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Regulates coat complex coatomer protein I (COPI)- independent Golgi-endoplasmic reticulum transport by recruiting the dynein-dynactin motor complex.;

Recessive Scores

pRec: 0.100

Intolerance Scores

LoFtool: 0.706
RVIS EVS: -1.51
RVIS percentile EVS: 3.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.821

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium