BICD1

Summary

BICD1 (BICD cargo adaptor 1, HGNC:1049) is a protein-coding gene on chromosome 12p11.21, encoding Protein bicaudal D homolog 1 (Q96G01). Regulates coat complex coatomer protein I (COPI)-independent Golgi-endoplasmic reticulum transport by recruiting the dynein-dynactin motor complex.

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.

Source: NCBI Gene 636 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 134 total
• MANE Select transcript: NM_001714

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1049
Approved symbol	BICD1
Name	BICD cargo adaptor 1
Location	12p11.21
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000151746
Ensembl biotype	protein_coding
OMIM	602204
Entrez	636

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 9 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000395758, ENST00000547680, ENST00000548411, ENST00000550207, ENST00000551086, ENST00000551848, ENST00000552160, ENST00000552226, ENST00000614004, ENST00000652176, ENST00000870313, ENST00000870314

RefSeq mRNA: 25 — MANE Select: NM_001714 NM_001003398, NM_001354186, NM_001354187, NM_001354188, NM_001363603, NM_001413155, NM_001413156, NM_001413157, NM_001413158, NM_001413159, NM_001413160, NM_001413161, NM_001413163, NM_001413164, NM_001413165, NM_001413166, NM_001413167, NM_001413168, NM_001413169, NM_001413171, NM_001413172, NM_001413180, NM_001413182, NM_001413183, NM_001714

CCDS: CCDS44859, CCDS86290, CCDS8726

Canonical transcript exons

ENST00000652176 — 10 exons

Exon	Start	End
ENSE00001001517	32293994	32294146
ENSE00001001518	32305697	32306122
ENSE00001158986	32334516	32334667
ENSE00001158991	32327461	32328555
ENSE00001159017	32216247	32216459
ENSE00001798510	32377540	32383633
ENSE00002317086	32337499	32337816
ENSE00002367683	32106847	32107544
ENSE00003495999	32367670	32367745
ENSE00003672738	32338786	32338979

Expression profiles

Bgee: expression breadth ubiquitous, 259 present calls, max score 97.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.2120 / max 1455.9636, expressed in 1746 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
124969	13.1215	1725
124970	2.1153	874
124971	0.4515	200
124975	0.2380	82
124968	0.1439	52
124974	0.1418	61

Top tissues by expression

290 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	97.13	gold quality
sural nerve	UBERON:0015488	96.15	gold quality
ganglionic eminence	UBERON:0004023	95.89	gold quality
cerebellar vermis	UBERON:0004720	94.79	gold quality
right uterine tube	UBERON:0001302	94.44	gold quality
caput epididymis	UBERON:0004358	91.72	gold quality
cortical plate	UBERON:0005343	91.20	gold quality
trigeminal ganglion	UBERON:0001675	91.12	gold quality
dorsal root ganglion	UBERON:0000044	90.84	gold quality
left ovary	UBERON:0002119	90.80	gold quality
paraflocculus	UBERON:0005351	90.55	gold quality
tibial nerve	UBERON:0001323	89.82	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.61	gold quality
right ovary	UBERON:0002118	89.33	gold quality
cerebellum	UBERON:0002037	88.48	gold quality
buccal mucosa cell	CL:0002336	88.38	gold quality
ovary	UBERON:0000992	88.31	gold quality
cerebellar cortex	UBERON:0002129	88.09	gold quality
cerebellar hemisphere	UBERON:0002245	87.97	gold quality
right hemisphere of cerebellum	UBERON:0014890	87.52	gold quality
lateral nuclear group of thalamus	UBERON:0002736	86.98	gold quality
Brodmann (1909) area 23	UBERON:0013554	86.23	gold quality
Brodmann (1909) area 46	UBERON:0006483	86.10	gold quality
embryo	UBERON:0000922	85.97	gold quality
endocervix	UBERON:0000458	85.43	gold quality
frontal pole	UBERON:0002795	85.29	gold quality
endometrium	UBERON:0001295	84.92	gold quality
substantia nigra pars compacta	UBERON:0001965	84.89	gold quality
primary visual cortex	UBERON:0002436	84.51	gold quality
pons	UBERON:0000988	84.28	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	25.06
E-ANND-3	yes	5.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

62 targeting BICD1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488
HSA-MIR-548Y	99.94	71.28	3514
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-3919	99.87	69.45	2489

Literature-anchored findings (GeneRIF, showing 16)

• Various processes in which BicD is involved during Drosophilian development (review) (PMID:16320833)
• findings show BICD1 localized to Chlamydia trachomatis inclusions in a biovar-specific manner and that EGFP-BICD1 is recruited to the inclusion in a microtubule- and Golgi apparatus-independent but chlamydial gene expression-dependent mechanism (PMID:17101644)
• These results imply that GSK-3beta may function in transporting centrosomal proteins to the centrosome by stabilizing the BICD1 and dynein complex, resulting in the regulation of a focused microtubule organization. (PMID:17139249)
• The brain-specific Rab6B via Bicaudal-D1 is linked to the dynein/dynactin complex, suggesting a regulatory role for Rab6B in the retrograde transport of cargo in neuronal cells. (PMID:17707369)
• BICD1 plays a similar role in telomere length homeostasis in humans. (PMID:18487243)
• the protease-activated receptor-1 interactor, Bicaudal D1, regulates G protein signaling and internalization (PMID:20164183)
• Variants in BICD1 are associated with length of telomeres, which suggests that a mechanism linked to accelerated aging may be involved in the pathogenesis of emphysema. (PMID:20709820)
• Graft BICD1 polymorphisms apart from the association with telomere length, affect early kidney function after transplantation (PMID:25792135)
• Kidney transplant recipients’ polymorphisms of genes associated with telomere length, BICD1 and chromosome 18, but not hTERT, affect kidney allograft early and long-term function after transplantation. (PMID:27496426)
• Data suggest that BICD1 and BICD2 are highly expressed in the nervous system during development and are important in neuronal homeostasis. [REVIEW] (PMID:28215293)
• This study showed that rs2735940 hTERT CX-TT donor-recipient genotype pair was associated with almost five times higher odds (OR=4.82; 95% CI: 1.32-18; p=0.016) of delayed graft function (DGF), and that rs2735940 hTERT, rs2630578 BICD1, and rs7235755 chromosome 18 polymorphisms combined pairs were not associated with acute rejection (AR). (PMID:28410362)
• BICD1 mediates HIF1alpha nuclear translocation in mesenchymal stem cells during hypoxia adaptation. (PMID:30464225)
• The disrupting Bicd1/Fignl1 interaction induced motor axon pathfinding defects characteristic of Fignl1 gain or loss of function, respectively. (PMID:31541015)
• BICD1 genes may contribute to the decrease in forced vital capacity levels by interacting with PM10 exposure (PMID:31846791)
• BICD1 functions as a prognostic biomarker and promotes hepatocellular carcinoma progression. (PMID:32088084)
• Biallelic Loss-of-Function Variants in BICD1 Are Associated with Peripheral Neuropathy and Hearing Loss. (PMID:37240244)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	bicd1a	ENSDARG00000079496
danio_rerio		ENSDARG00000098551
mus_musculus	Bicd1	ENSMUSG00000003452
rattus_norvegicus	Bicd1	ENSRNOG00000036911
drosophila_melanogaster	BicD	FBGN0000183
caenorhabditis_elegans		WBGENE00016611

Paralogs (1): BICD2 (ENSG00000185963)

Protein

Protein identifiers

Protein bicaudal D homolog 1 — Q96G01 (reviewed: Q96G01)

All UniProt accessions (6): Q96G01, A0A087WYJ7, A8MVZ6, F8VZX7, F8W056, U3KQF7

UniProt curated annotations — full annotation on UniProt →

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

Subunit / interactions. Interacts with RAB6A. Interacts (via C-terminus) with RAB6B (GTP-bound); the interaction is direct. Interacts with CLIP-115 and KIFC2. (Microbial infection) Interacts with human cytomegalovirus/HHV-5 protein UL32.

Subcellular location. Golgi apparatus.

Tissue specificity. Expressed in the brain, heart and skeletal muscle.

Miscellaneous. Due to intron retention. Due to intron retention.

Similarity. Belongs to the BicD family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q96G01-1	1	yes
Q96G01-2	2
Q96G01-3	3
Q96G01-4	4

RefSeq proteins (25): NP_001003398, NP_001341115, NP_001341116, NP_001341117, NP_001350532, NP_001400084, NP_001400085, NP_001400086, NP_001400087, NP_001400088, NP_001400089, NP_001400090, NP_001400092, NP_001400093, NP_001400094, NP_001400095, NP_001400096, NP_001400097, NP_001400098, NP_001400100, NP_001400101, NP_001400109, NP_001400111, NP_001400112, NP_001705* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018477	BICD	Family

Pfam: PF09730

UniProt features (24 total): region of interest 6, splice variant 6, compositionally biased region 4, sequence conflict 3, coiled-coil region 3, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96G01-F1	72.36	0.44

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-6811436	COPI-independent Golgi-to-ER retrograde traffic
R-HSA-199991	Membrane Trafficking
R-HSA-5653656	Vesicle-mediated transport
R-HSA-6811442	Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-8856688	Golgi-to-ER retrograde transport

MSigDB gene sets: 217 (showing top): RRAGTTGT_UNKNOWN, GOBP_PROTEIN_LOCALIZATION_TO_CYTOSKELETON, BROWNE_HCMV_INFECTION_6HR_DN, GOBP_POSITIVE_REGULATION_OF_ENDOCYTOSIS, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_DN, GOBP_MICROTUBULE_ANCHORING, GOZGIT_ESR1_TARGETS_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, YANG_BREAST_CANCER_ESR1_LASER_DN, GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_ORGANELLE_TRANSPORT_ALONG_MICROTUBULE, GOMF_GTPASE_BINDING

GO Biological Process (12): RNA processing (GO:0006396), intracellular mRNA localization (GO:0008298), anatomical structure morphogenesis (GO:0009653), virion assembly (GO:0019068), stress granule assembly (GO:0034063), constitutive secretory pathway (GO:0045054), positive regulation of receptor-mediated endocytosis (GO:0048260), regulation of microtubule cytoskeleton organization (GO:0070507), minus-end-directed organelle transport along microtubule (GO:0072385), microtubule anchoring at microtubule organizing center (GO:0072393), negative regulation of phospholipase C-activating G protein-coupled receptor signaling pathway (GO:1900737), positive regulation of protein localization to centrosome (GO:1904781)

GO Molecular Function (9): structural constituent of cytoskeleton (GO:0005200), cytoskeletal adaptor activity (GO:0008093), protein kinase binding (GO:0019901), small GTPase binding (GO:0031267), proteinase activated receptor binding (GO:0031871), dynactin binding (GO:0034452), dynein intermediate chain binding (GO:0045505), dynein complex binding (GO:0070840), protein binding (GO:0005515)

GO Cellular Component (10): Golgi apparatus (GO:0005794), trans-Golgi network (GO:0005802), centrosome (GO:0005813), cytosol (GO:0005829), cytoskeleton (GO:0005856), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410), perinuclear region of cytoplasm (GO:0048471), secretory vesicle (GO:0099503), cytoplasmic microtubule (GO:0005881)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Golgi-to-ER retrograde transport	1
Vesicle-mediated transport	1
Membrane Trafficking	1
Intra-Golgi and retrograde Golgi-to-ER traffic	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	5
cellular anatomical structure	3
cytoskeletal protein binding	2
gene expression	1
RNA biosynthetic process	1
primary metabolic process	1
RNA localization	1
developmental process	1
anatomical structure development	1
viral process	1
viral life cycle	1
membraneless organelle assembly	1
exocytosis	1
receptor-mediated endocytosis	1
positive regulation of endocytosis	1
regulation of receptor-mediated endocytosis	1
microtubule cytoskeleton organization	1
regulation of microtubule-based process	1
regulation of cytoskeleton organization	1
organelle transport along microtubule	1
microtubule anchoring	1
phospholipase C-activating G protein-coupled receptor signaling pathway	1
negative regulation of G protein-coupled receptor signaling pathway	1
regulation of phospholipase C-activating G protein-coupled receptor signaling pathway	1
protein localization to centrosome	1
positive regulation of protein localization	1
regulation of protein localization to centrosome	1
structural molecule activity	1
cytoskeleton	1
cytoskeleton organization	1
protein-macromolecule adaptor activity	1
kinase binding	1
GTPase binding	1
G protein-coupled receptor binding	1
protein binding	1
protein-containing complex binding	1
binding	1
endomembrane system	1
intracellular membrane-bounded organelle	1
Golgi apparatus subcompartment	1

Protein interactions and networks

STRING

1168 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BICD1	RAB6A	P20340	933
BICD1	DDX11	Q96FC9	853
BICD1	CELF4	Q9BZC1	838
BICD1	PIK3C3	Q8NEB9	737
BICD1	BICDL1	Q6ZP65	698
BICD1	DCTN2	Q13561	666
BICD1	DYNC1H1	Q14204	660
BICD1	HOOK3	Q86VS8	657
BICD1	DYNLL1	P63167	644
BICD1	BICDL2	A1A5D9	603
BICD1	FMR1	Q06787	560
BICD1	NDE1	Q9NXR1	556
BICD1	NDEL1	Q9GZM8	555
BICD1	NEK9	Q8TD19	543
BICD1	DYNC1LI1	Q9Y6G9	529

IntAct

37 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
GSK3B	BICD1	psi-mi:“MI:0407”(direct interaction)	0.670
BICD1	GSK3B	psi-mi:“MI:0915”(physical association)	0.670
GSK3B	BICD1	psi-mi:“MI:0915”(physical association)	0.670
NEFL	RABEP1	psi-mi:“MI:0914”(association)	0.530
STAT3	BICD1	psi-mi:“MI:0915”(physical association)	0.510
BICD1	STAT3	psi-mi:“MI:0915”(physical association)	0.510
DCTN1	BICD1	psi-mi:“MI:0403”(colocalization)	0.430
BICD1	NPM1	psi-mi:“MI:0915”(physical association)	0.400
H1-5	BICD1	psi-mi:“MI:0915”(physical association)	0.400
NIN	BICD1	psi-mi:“MI:0915”(physical association)	0.400
BICD1		psi-mi:“MI:0915”(physical association)	0.370
BICD1	FXR1	psi-mi:“MI:0915”(physical association)	0.370
MAPK14	BICD1	psi-mi:“MI:0915”(physical association)	0.370
PLK1	ERCC6L	psi-mi:“MI:0914”(association)	0.350
	CCDC22	psi-mi:“MI:0914”(association)	0.350
ESR2		psi-mi:“MI:0914”(association)	0.350
MAPRE1	SCAMP1	psi-mi:“MI:0914”(association)	0.350
SCHIP1	VWA8	psi-mi:“MI:0914”(association)	0.350
BICD2	RGPD8	psi-mi:“MI:0914”(association)	0.350
SH3BP5L	PPP1R12A	psi-mi:“MI:0914”(association)	0.350
SYBU	SNPH	psi-mi:“MI:0914”(association)	0.350
BICD2	HERC2	psi-mi:“MI:0914”(association)	0.350
BICD1	DYNC1I1	psi-mi:“MI:0914”(association)	0.350
BICD1	TUBG1	psi-mi:“MI:0403”(colocalization)	0.350
CEP128	CCDC66	psi-mi:“MI:2364”(proximity)	0.270
PCM1	CCDC66	psi-mi:“MI:2364”(proximity)	0.270
FGFR4	SH3PXD2B	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (257): BICD1 (Two-hybrid), RAB6A (Two-hybrid), BICD1 (Reconstituted Complex), BICD1 (Affinity Capture-MS), BICD1 (Affinity Capture-MS), BICD1 (Proximity Label-MS), BICD1 (Proximity Label-MS), BICD1 (Affinity Capture-MS), BICD1 (Affinity Capture-MS), BICD1 (Affinity Capture-MS), BICD1 (Affinity Capture-RNA), BICD1 (Proximity Label-MS), BICD1 (Affinity Capture-RNA), BICD1 (Proximity Label-MS), BICD1 (Proximity Label-MS)

ESM2 similar proteins: A0PJP4, A0PJT0, A2VDP1, A4IFK7, D3ZUQ0, E9PSL7, O14578, O75665, P0C219, P49025, P97817, Q01850, Q0IHE5, Q14BN4, Q17QG3, Q28623, Q3LGD4, Q3SYW5, Q3URD3, Q3V079, Q4R3X1, Q4R7Y8, Q58A65, Q5DTM8, Q5EBL4, Q5R5R4, Q5VTR2, Q5ZJA3, Q5ZLS3, Q62172, Q62796, Q68CZ1, Q6AYA0, Q6DFC2, Q6DH86, Q6NRH3, Q6ZUS6, Q7Z3E2, Q86VS8, Q8BR07

Diamond homologs: P16568, Q8BR07, Q8TD16, Q921C5, Q96G01, V6CJ04

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
GSK3B	“up-regulates activity”	BICD1	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 40 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Loss of Nlp from mitotic centrosomes	5	28.3×	7e-05
Loss of proteins required for interphase microtubule organization from the centrosome	5	28.3×	7e-05
Regulation of PLK1 Activity at G2/M Transition	6	27.2×	2e-05
AURKA Activation by TPX2	5	27.2×	7e-05
Recruitment of mitotic centrosome proteins and complexes	5	24.3×	1e-04
Recruitment of NuMA to mitotic centrosomes	5	20.8×	2e-04
Anchoring of the basal body to the plasma membrane	5	20.2×	2e-04
Mitotic Prometaphase	5	12.4×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

134 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	110
Likely benign	4
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

4112 predictions. Top by Δscore:

Variant	Effect	Δscore
12:32107540:AAGAG:A	donor_gain	1.0000
12:32107541:AGAG:A	donor_gain	1.0000
12:32107541:AGAGG:A	donor_loss	1.0000
12:32107542:GAG:G	donor_gain	1.0000
12:32107542:GAGG:G	donor_gain	1.0000
12:32107543:AG:A	donor_gain	1.0000
12:32107544:GG:G	donor_gain	1.0000
12:32107544:GGTG:G	donor_loss	1.0000
12:32107545:G:GG	donor_gain	1.0000
12:32107545:GT:G	donor_loss	1.0000
12:32127702:G:GT	donor_gain	1.0000
12:32127702:G:T	donor_gain	1.0000
12:32127755:A:AG	donor_gain	1.0000
12:32216234:A:AG	acceptor_gain	1.0000
12:32216235:T:G	acceptor_gain	1.0000
12:32216236:A:AG	acceptor_gain	1.0000
12:32216237:T:G	acceptor_gain	1.0000
12:32216238:A:AG	acceptor_gain	1.0000
12:32216238:ACTCT:A	acceptor_gain	1.0000
12:32216239:C:G	acceptor_gain	1.0000
12:32216242:T:TA	acceptor_gain	1.0000
12:32216244:CAG:C	acceptor_loss	1.0000
12:32216245:A:AC	acceptor_loss	1.0000
12:32216245:A:AG	acceptor_gain	1.0000
12:32216245:AG:A	acceptor_gain	1.0000
12:32216246:G:GT	acceptor_gain	1.0000
12:32216246:GG:G	acceptor_gain	1.0000
12:32216246:GGC:G	acceptor_gain	1.0000
12:32216246:GGCA:G	acceptor_gain	1.0000
12:32216246:GGCAT:G	acceptor_gain	1.0000

AlphaMissense

6415 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:32107390:T:C	L20P	1.000
12:32107402:T:C	L24P	1.000
12:32107431:G:C	A34P	1.000
12:32107434:G:C	A35P	1.000
12:32107435:C:A	A35D	1.000
12:32107443:G:A	G38R	1.000
12:32107443:G:C	G38R	1.000
12:32107443:G:T	G38W	1.000
12:32107444:G:A	G38E	1.000
12:32107447:T:C	L39P	1.000
12:32107456:T:C	L42P	1.000
12:32327989:A:C	S512R	1.000
12:32327991:T:A	S512R	1.000
12:32327991:T:G	S512R	1.000
12:32328001:G:C	A516P	1.000
12:32328002:C:A	A516D	1.000
12:32328008:T:C	L518P	1.000
12:32328010:T:G	Y519D	1.000
12:32328017:A:C	H521P	1.000
12:32328022:T:C	C523R	1.000
12:32328024:T:G	C523W	1.000
12:32328043:C:T	P530S	1.000
12:32328044:C:A	P530H	1.000
12:32328059:T:C	L535P	1.000
12:32328338:T:C	L628P	1.000
12:32328359:A:C	Q635P	1.000
12:32328371:T:C	L639P	1.000
12:32328379:G:C	A642P	1.000
12:32328485:T:C	L677P	1.000
12:32328506:A:T	K684I	1.000

dbSNP variants (sampled 300 via entrez): RS1000001653 (12:32140932 T>A), RS1000006208 (12:32186481 A>C), RS1000007423 (12:32377440 G>A), RS1000012860 (12:32368335 C>A,T), RS1000015647 (12:32234915 G>A), RS1000038521 (12:32377136 C>T), RS1000062470 (12:32123383 A>C), RS1000074479 (12:32168739 G>T), RS1000081146 (12:32228437 A>G), RS1000088826 (12:32194444 C>G), RS1000091933 (12:32321929 G>A,C), RS1000097779 (12:32288699 C>G,T), RS1000118329 (12:32138074 C>T), RS1000137770 (12:32186139 A>G), RS1000138611 (12:32111855 A>G)

Disease associations

OMIM: gene MIM:602204 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST000268_5	Normalized brain volume	4.000000e-06
GCST000745_11	Pancreatic cancer	3.000000e-07
GCST000770_6	Emphysema-related traits	6.000000e-07
GCST001762_485	Obesity-related traits	7.000000e-06
GCST009255_10	Fourth ventricle volume	4.000000e-06
GCST009835_3	Left ventricular mass x antihypertensive treatment interaction	1.000000e-07
GCST010991_13	Parkinson’s disease	4.000000e-08
GCST012006_5	Intralaminar thalamic nuclei volume	4.000000e-10

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0005116	urinary metabolite measurement
EFO:0005405	response to antihypertensive drug
EFO:0009289	left ventricular mass
EFO:0006935	thalamus volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

53 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	4
Benzo(a)pyrene	decreases expression, increases expression, increases methylation	3
Estradiol	affects cotreatment, decreases expression, increases expression	3
methylmercuric chloride	decreases expression, increases expression	2
entinostat	increases expression, affects cotreatment	2
Air Pollutants	increases abundance, increases expression, increases response to substance	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tretinoin	decreases expression	2
Particulate Matter	increases abundance, increases expression, increases response to substance	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
trichostatin A	decreases expression	1
beta-lapachone	decreases expression	1
sodium arsenite	increases expression	1
CGP 52608	affects binding, increases reaction	1
monomethylarsonous acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	1
abrine	increases expression	1
dorsomorphin	increases expression, decreases expression, affects cotreatment	1
bisphenol S	decreases methylation	1
jinfukang	affects cotreatment, decreases expression	1
PCI 5002	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Vorinostat	decreases expression	1
Acetaminophen	affects expression	1
Arsenic	affects methylation	1
Atrazine	decreases expression	1
Azacitidine	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.