BICD1
BICD cargo adaptor 1
Basic information
Region (hg38): 12:32106834-32383633
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (15 variants)
- not specified (2 variants)
- not provided (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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 4 | ||||
| missense | 15 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 15 | 0 | 4 |
Variants in BICD1
This is a list of pathogenic ClinVar variants found in the BICD1 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-32107396-A-G | Inborn genetic diseases | Uncertain significance (Jan 04, 2022) | ||
| 12-32107418-C-G | Inborn genetic diseases | Uncertain significance (Jun 28, 2023) | ||
| 12-32107445-G-A | Benign (Mar 29, 2018) | |||
| 12-32107519-A-G | Inborn genetic diseases | Uncertain significance (Dec 16, 2022) | ||
| 12-32216297-G-C | Inborn genetic diseases | Uncertain significance (Aug 14, 2023) | ||
| 12-32216354-G-A | Benign (Jul 16, 2018) | |||
| 12-32216379-C-A | Inborn genetic diseases | Uncertain significance (Dec 21, 2022) | ||
| 12-32216425-A-G | Inborn genetic diseases | Uncertain significance (Aug 14, 2023) | ||
| 12-32305742-G-C | Inborn genetic diseases | Uncertain significance (Jun 24, 2022) | ||
| 12-32305776-C-T | Inborn genetic diseases | Uncertain significance (Jul 13, 2022) | ||
| 12-32327475-G-T | Inborn genetic diseases | Uncertain significance (Aug 23, 2021) | ||
| 12-32327540-C-T | Inborn genetic diseases | Uncertain significance (Sep 09, 2021) | ||
| 12-32327562-C-A | Inborn genetic diseases | Uncertain significance (Jul 20, 2021) | ||
| 12-32327816-A-C | Inborn genetic diseases | Uncertain significance (May 24, 2023) | ||
| 12-32327830-A-C | Inborn genetic diseases | Uncertain significance (May 06, 2022) | ||
| 12-32327840-A-G | Inborn genetic diseases | Uncertain significance (Nov 12, 2021) | ||
| 12-32327858-G-A | Inborn genetic diseases | Uncertain significance (Jul 19, 2022) | ||
| 12-32327882-G-A | Inborn genetic diseases | Uncertain significance (Dec 08, 2022) | ||
| 12-32328118-C-G | Inborn genetic diseases | Uncertain significance (Sep 17, 2021) | ||
| 12-32328159-G-C | not specified | Benign (Mar 28, 2016) | ||
| 12-32328311-G-A | Inborn genetic diseases | Uncertain significance (Feb 16, 2023) | ||
| 12-32328385-G-C | Inborn genetic diseases | Uncertain significance (Jan 25, 2023) | ||
| 12-32328435-C-T | not specified | Benign (Mar 28, 2016) | ||
| 12-32337693-T-C | Inborn genetic diseases | Uncertain significance (Jan 25, 2023) | ||
| 12-32337695-G-A | Inborn genetic diseases | Uncertain significance (Apr 26, 2023) |
GnomAD
Source:
| 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:
- 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