BICD1

BICD cargo adaptor 1

Basic information

Region (hg38): 12:32106834-32383633

Links

ENSG00000151746 ∙ NCBI:636 ∙ OMIM:602204 ∙ HGNC:1049 ∙ Uniprot:Q96G01 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BICD1 gene.

• Inborn genetic diseases (24 variants)
• not provided (3 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BICD1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					4	4
missense			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	24	1	4

Variants in BICD1

This is a list of pathogenic ClinVar variants found in the BICD1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-32107396-A-G		not specified	Uncertain significance (Jan 04, 2022)
12-32107418-C-G		not specified	Uncertain significance (Jun 28, 2023)
12-32107445-G-A			Benign (Mar 29, 2018)
12-32107477-A-C		not specified	Uncertain significance (Jan 16, 2024)
12-32107483-A-G		not specified	Uncertain significance (Jan 02, 2024)
12-32107519-A-G		not specified	Uncertain significance (Dec 16, 2022)
12-32107615-CAAG-C			Likely benign (Dec 01, 2022)
12-32216297-G-C		not specified	Uncertain significance (Aug 14, 2023)
12-32216354-G-A			Benign (Jul 16, 2018)
12-32216379-C-A		not specified	Uncertain significance (Dec 21, 2022)
12-32216424-G-A		not specified	Uncertain significance (Aug 12, 2021)
12-32216425-A-G		not specified	Uncertain significance (Aug 14, 2023)
12-32216436-G-T		not specified	Uncertain significance (Nov 09, 2023)
12-32305742-G-C		not specified	Uncertain significance (Jun 24, 2022)
12-32305776-C-T		not specified	Uncertain significance (Jul 13, 2022)
12-32305795-T-G		not specified	Uncertain significance (Jan 22, 2024)
12-32306069-T-G		not specified	Uncertain significance (Jan 22, 2024)
12-32327475-G-T		not specified	Uncertain significance (Aug 23, 2021)
12-32327540-C-T		not specified	Uncertain significance (Sep 09, 2021)
12-32327562-C-A		not specified	Uncertain significance (Jul 20, 2021)
12-32327816-A-C		not specified	Uncertain significance (May 24, 2023)
12-32327830-A-C		not specified	Uncertain significance (May 06, 2022)
12-32327840-A-G		not specified	Uncertain significance (Nov 12, 2021)
12-32327858-G-A		not specified	Uncertain significance (Jul 19, 2022)
12-32327882-G-A		not specified	Uncertain significance (Dec 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BICD1	protein_coding	protein_coding	ENST00000281474	10	276799

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000157	1.00	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.27	397	546	0.727	0.0000309	6393
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000520	0.000520
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000110	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000164	0.000158
Middle Eastern	0.000110	0.000109
South Asian	0.0000665	0.0000653
Other	0.000359	0.000326

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.706
• rvis_EVS: -1.51
• rvis_percentile_EVS: 3.54

Haploinsufficiency Scores

• pHI: 0.310
• hipred: Y
• hipred_score: 0.663
• ghis: 0.669

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.821

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bicd1
• Phenotype: homeostasis/metabolism phenotype; hearing/vestibular/ear phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: RNA processing;intracellular mRNA localization;anatomical structure morphogenesis;viral process;protein localization to organelle;stress granule assembly;positive regulation of receptor-mediated endocytosis;regulation of microtubule cytoskeleton organization;minus-end-directed organelle transport along microtubule;microtubule anchoring at microtubule organizing center;negative regulation of phospholipase C activity;regulation of proteinase activated receptor activity;negative regulation of phospholipase C-activating G protein-coupled receptor signaling pathway;positive regulation of protein localization to centrosome
• Cellular component: Golgi apparatus;trans-Golgi network;centrosome;cytosol;cytoskeleton;cytoplasmic microtubule;membrane;cytoplasmic vesicle;tubulin complex;perinuclear region of cytoplasm;host cell viral assembly compartment
• Molecular function: structural constituent of cytoskeleton;protein binding;cytoskeletal adaptor activity;Rab GTPase binding;protein kinase binding;proteinase activated receptor binding;dynactin binding;dynein intermediate chain binding;dynein complex binding