BICDL1

Summary

BICDL1 (BICD family like cargo adaptor 1, HGNC:28095) is a protein-coding gene on chromosome 12q24.23, encoding BICD family-like cargo adapter 1 (Q6ZP65). 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.

Predicted to enable dynactin binding activity and small GTPase binding activity. Predicted to be involved in Golgi to secretory granule transport; neuron projection development; and vesicle transport along microtubule. Predicted to be located in centrosome.

Source: NCBI Gene 92558 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 14 total — 1 likely-pathogenic
• MANE Select transcript: NM_001367886

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28095
Approved symbol	BICDL1
Name	BICD family like cargo adaptor 1
Location	12q24.23
Locus type	gene with protein product
Status	Approved
Aliases	FLJ26450, BICDR-1
Ensembl gene	ENSG00000135127
Ensembl biotype	protein_coding
OMIM	617002
Entrez	92558

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 11 protein_coding, 4 retained_intron, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000397558, ENST00000546420, ENST00000546460, ENST00000546502, ENST00000546790, ENST00000546857, ENST00000546861, ENST00000547841, ENST00000548673, ENST00000550197, ENST00000550245, ENST00000926851, ENST00000926852, ENST00000926853, ENST00000926854, ENST00000926855, ENST00000926856, ENST00000959873, ENST00000959874, ENST00000959875

RefSeq mRNA: 2 — MANE Select: NM_001367886 NM_001367886, NM_207311

CCDS: CCDS41845, CCDS91757

Canonical transcript exons

ENST00000548673 — 10 exons

Exon	Start	End
ENSE00000918209	120074443	120074586
ENSE00000918210	120072511	120072729
ENSE00001529201	120093000	120094494
ENSE00002203755	119998521	119998736
ENSE00002235935	120061710	120061826
ENSE00003468567	120080887	120081017
ENSE00003608844	120089951	120090071
ENSE00003613774	120071622	120071801
ENSE00003694015	120064733	120064879
ENSE00003933406	119989236	119990297

Expression profiles

Bgee: expression breadth ubiquitous, 235 present calls, max score 98.77.

FANTOM5 (CAGE): breadth broad, TPM avg 6.9531 / max 344.5600, expressed in 849 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
128310	5.7402	822
128311	1.0525	300
128315	0.0728	17
128312	0.0608	28
128314	0.0217	8
128316	0.0052	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
metanephros cortex	UBERON:0010533	98.77	gold quality
renal medulla	UBERON:0000362	98.36	gold quality
lower esophagus mucosa	UBERON:0035834	96.79	gold quality
pituitary gland	UBERON:0000007	96.45	gold quality
right hemisphere of cerebellum	UBERON:0014890	96.45	gold quality
skin of abdomen	UBERON:0001416	96.19	gold quality
adenohypophysis	UBERON:0002196	95.76	gold quality
skin of leg	UBERON:0001511	95.64	gold quality
cerebellar hemisphere	UBERON:0002245	95.56	gold quality
right testis	UBERON:0004534	95.53	gold quality
cerebellar cortex	UBERON:0002129	95.37	gold quality
left testis	UBERON:0004533	95.20	gold quality
right frontal lobe	UBERON:0002810	94.34	gold quality
cerebellum	UBERON:0002037	93.30	gold quality
zone of skin	UBERON:0000014	93.00	gold quality
cortical plate	UBERON:0005343	92.53	gold quality
esophagus mucosa	UBERON:0002469	92.40	gold quality
testis	UBERON:0000473	91.89	gold quality
germinal epithelium of ovary	UBERON:0001304	91.63	gold quality
adult mammalian kidney	UBERON:0000082	91.40	gold quality
pigmented layer of retina	UBERON:0001782	91.24	gold quality
granulocyte	CL:0000094	89.42	gold quality
right lobe of thyroid gland	UBERON:0001119	89.27	gold quality
Brodmann (1909) area 9	UBERON:0013540	89.12	gold quality
lymph node	UBERON:0000029	88.99	gold quality
cingulate cortex	UBERON:0003027	88.89	gold quality
anterior cingulate cortex	UBERON:0009835	88.76	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	88.56	gold quality
left lobe of thyroid gland	UBERON:0001120	88.49	gold quality
upper leg skin	UBERON:0004262	87.67	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.23

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

103 targeting BICDL1, 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-3924	100.00	72.09	2394
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-221-3P	99.86	71.56	1329
HSA-MIR-222-3P	99.86	71.35	1337
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-4699-3P	99.71	70.15	3142

Literature-anchored findings (GeneRIF, showing 1)

• CCDC64 is a target gene of the BACH1 transcription factor according to ChIP-seq analysis in HEK 293 cells. (PMID:21555518)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	bicdl1	ENSDARG00000074761
mus_musculus	Bicdl1	ENSMUSG00000041609
rattus_norvegicus	Bicdl1	ENSRNOG00000056955
drosophila_melanogaster	CG32137	FBGN0052137

Paralogs (2): SPDL1 (ENSG00000040275), BICDL2 (ENSG00000162069)

Protein

Protein identifiers

BICD family-like cargo adapter 1 — Q6ZP65 (reviewed: Q6ZP65)

Alternative names: Bicaudal D-related protein 1, Coiled-coil domain-containing protein 64A

All UniProt accessions (4): Q6ZP65, H0YHP2, H0YHW1, H0YIC1

UniProt curated annotations — full annotation on UniProt →

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 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). Predominantly recruits 2 dyneins, which increases both the force and speed of the microtubule motor. Component of secretory vesicle machinery in developing neurons that acts as a regulator of neurite outgrowth. Regulates the secretory vesicle transport by controlling the accumulation of Rab6-containing secretory vesicles in the pericentrosomal region restricting anterograde secretory transport during the early phase of neuronal differentiation, thereby inhibiting neuritogenesis.

Subunit / interactions. Part of a tripartite complex with dynein and dynactin, acts an adapter linking the dynein motor complex and dynactin. Interacts with KIF1C. Interacts with RAB6A and RAB6B; interaction is specific to Rab6.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome.

Similarity. Belongs to the BICDR family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6ZP65-1	1	yes
Q6ZP65-2	2

RefSeq proteins (2): NP_001354815, NP_997194 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR051149	Spindly/BICDR_Dynein_Adapter	Family

UniProt features (11 total): region of interest 2, coiled-coil region 2, compositionally biased region 2, splice variant 2, chain 1, sequence conflict 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZP65-F1	77.15	0.53

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 196 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, RRAGTTGT_UNKNOWN, AP1_01, GOBP_VESICLE_LOCALIZATION, GCANCTGNY_MYOD_Q6, AREB6_03, GOBP_NEUROGENESIS, GOBP_ORGANELLE_TRANSPORT_ALONG_MICROTUBULE, GOMF_GTPASE_BINDING, GOCC_MICROTUBULE_ORGANIZING_CENTER, AP1_Q4_01, GOBP_VESICLE_CYTOSKELETAL_TRAFFICKING, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2, BACH2_01, MARTIN_NFKB_TARGETS_UP

GO Biological Process (4): neuron projection development (GO:0031175), vesicle transport along microtubule (GO:0047496), Golgi to secretory granule transport (GO:0055107), nervous system development (GO:0007399)

GO Molecular Function (2): small GTPase binding (GO:0031267), dynactin binding (GO:0034452)

GO Cellular Component (3): centrosome (GO:0005813), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
neuron development	1
plasma membrane bounded cell projection organization	1
organelle transport along microtubule	1
vesicle cytoskeletal trafficking	1
intercellular transport	1
intracellular transport	1
system development	1
GTPase binding	1
cytoskeletal protein binding	1
centriole	1
microtubule organizing center	1
intracellular anatomical structure	1
cellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

648 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BICDL1	RAB6A	P20340	887
BICDL1	BICD2	Q8TD16	831
BICDL1	HOOK3	Q86VS8	822
BICDL1	KIF1C	O43896	792
BICDL1	NINL	Q9Y2I6	761
BICDL1	RAB11FIP3	O75154	730
BICDL1	HOOK1	Q9UJC3	699
BICDL1	BICD1	Q96G01	698
BICDL1	NIN	Q8N4C6	639
BICDL1	RASEF	Q8IZ41	526
BICDL1	CRACR2A	Q9BSW2	490
BICDL1	CCDC125	Q86Z20	485
BICDL1	TRAK2	O60296	482
BICDL1	KIF20A	O95235	467
BICDL1	CFAP184	Q2M329	460

IntAct

4 interactions, top by confidence:

A	B	Type	Score
HSPB1	BICDL1	psi-mi:“MI:0915”(physical association)	0.370
PB2		psi-mi:“MI:0914”(association)	0.350
CSNK2B	TUBAL3	psi-mi:“MI:0914”(association)	0.350

BioGRID (5): CCDC64 (Two-hybrid), CCDC64 (Positive Genetic), NEFM (Cross-Linking-MS (XL-MS)), EEA1 (Cross-Linking-MS (XL-MS)), GNPAT (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0JMK8, A0JNT9, A2AIV8, A6NI79, A9QT41, B2RZ86, B3DLE8, B8JK76, B9V5F5, F1R4Y7, O35550, O35551, O88522, P0CF95, Q08DR9, Q0IHN7, Q0V9T6, Q15276, Q29RS0, Q2MJU7, Q3KR99, Q3SWS9, Q502I3, Q5BIX7, Q5HZK9, Q5U4E6, Q60952, Q6DCD4, Q6DIX6, Q6GLX3, Q6NRW2, Q6P402, Q6PGZ0, Q6TMG5, Q6ZP65, Q6ZU80, Q86SQ7, Q8BI22, Q8BVL9, Q8CHW5

Diamond homologs: A0JNT9, P0CF95, Q0V9T6, Q6DIX6, Q6GLX3, Q6ZP65, Q8CHW5, A1A5D9, Q8SWR2, A0JMK8

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
BICDL1	“up-regulates activity”	KIF1C	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1527741	GRCh37/hg19 12q24.23-24.31(chr12:118486842-120995382)	Likely pathogenic

SpliceAI

2892 predictions. Top by Δscore:

Variant	Effect	Δscore
12:119990294:CGAGG:C	donor_loss	1.0000
12:119990295:GAG:G	donor_gain	1.0000
12:119990296:AGG:A	donor_loss	1.0000
12:119990297:GGT:G	donor_loss	1.0000
12:119990298:G:C	donor_loss	1.0000
12:119990298:G:GG	donor_gain	1.0000
12:119998519:A:AG	acceptor_gain	1.0000
12:119998520:G:GG	acceptor_gain	1.0000
12:119998520:GC:G	acceptor_gain	1.0000
12:120071616:T:A	acceptor_gain	1.0000
12:120071619:A:AG	acceptor_gain	1.0000
12:120071620:A:G	acceptor_gain	1.0000
12:120071621:G:GG	acceptor_gain	1.0000
12:120071621:GCT:G	acceptor_gain	1.0000
12:120071621:GCTGC:G	acceptor_gain	1.0000
12:120071772:GC:G	donor_gain	1.0000
12:120071798:GCAG:G	donor_gain	1.0000
12:120071798:GCAGG:G	donor_loss	1.0000
12:120071799:CAGGT:C	donor_loss	1.0000
12:120071800:AGGTG:A	donor_loss	1.0000
12:120071801:GGTGC:G	donor_loss	1.0000
12:120071802:G:T	donor_loss	1.0000
12:120071803:T:G	donor_loss	1.0000
12:120080882:GTTA:G	acceptor_loss	1.0000
12:120080884:TAG:T	acceptor_loss	1.0000
12:120080885:A:AG	acceptor_gain	1.0000
12:120080885:AGGT:A	acceptor_gain	1.0000
12:120080885:AGGTG:A	acceptor_loss	1.0000
12:120080886:G:GT	acceptor_gain	1.0000
12:120080886:GGT:G	acceptor_gain	1.0000

AlphaMissense

4036 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:119990217:G:C	G117R	0.999
12:119990218:G:A	G117D	0.999
12:119990227:T:C	L120P	0.999
12:119998600:T:C	L170P	0.999
12:119998717:T:C	L209P	0.999
12:120061732:T:C	L223P	0.999
12:120072686:T:C	L422P	0.999
12:120080999:G:C	R474P	0.999
12:120081007:G:C	A477P	0.999
12:120090024:G:C	A505P	0.999
12:120090046:T:C	L512P	0.999
12:120090058:T:C	L516P	0.999
12:120090066:T:A	W519R	0.999
12:120090066:T:C	W519R	0.999
12:119990197:T:C	L110P	0.998
12:119990208:G:C	A114P	0.998
12:119990223:G:C	A119P	0.998
12:119990230:T:C	L121P	0.998
12:119998621:T:C	L177P	0.998
12:119998696:T:C	L202P	0.998
12:119998729:T:C	L213P	0.998
12:120061816:T:C	L251P	0.998
12:120090016:T:C	L502S	0.998
12:120090040:T:C	L510P	0.998
12:120090063:G:C	A518P	0.998
12:120090068:G:C	W519C	0.998
12:120090068:G:T	W519C	0.998
12:119990209:C:A	A114D	0.997
12:119990215:T:C	L116P	0.997
12:119990218:G:T	G117V	0.997

dbSNP variants (sampled 300 via entrez): RS1000000512 (12:120044908 A>G), RS1000033170 (12:120044648 A>G), RS1000041220 (12:120003139 C>A), RS1000077130 (12:120062822 T>C), RS1000083142 (12:120016877 T>C), RS1000087537 (12:120089244 C>T), RS1000121048 (12:120094819 G>A), RS1000167207 (12:119999839 C>G,T), RS1000169968 (12:120087632 C>A,T), RS1000199514 (12:120067585 G>A), RS1000253672 (12:120008487 G>T), RS1000260668 (12:119999574 C>T), RS1000283241 (12:120057965 G>A), RS1000318222 (12:120039301 A>T), RS1000321057 (12:120082495 C>A,G,T)

Disease associations

OMIM: gene MIM:617002 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST000477_19	Cognitive performance	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0003926	neuropsychological test

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	4
bisphenol A	affects expression, decreases methylation	2
titanium dioxide	decreases methylation	1
terbufos	increases methylation	1
sodium arsenite	decreases expression	1
benzo(e)pyrene	increases methylation	1
perfluorooctane sulfonic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, increases expression	1
dorsomorphin	affects cotreatment, decreases expression, increases expression	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	increases expression	1
Sunitinib	increases expression	1
Zoledronic Acid	increases expression	1
Leflunomide	increases expression	1
Cadmium	decreases expression, increases abundance	1
Calcitriol	affects cotreatment, increases expression	1
Chelating Agents	affects binding, increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Copper	affects binding, increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Fonofos	increases methylation	1
Estradiol	decreases expression	1
Mercuric Chloride	affects cotreatment, decreases expression	1
Methapyrilene	increases methylation	1
Methyl Methanesulfonate	increases expression	1
Parathion	increases methylation	1
Selenium	increases expression	1
Smoke	decreases expression	1
Testosterone	affects cotreatment, increases expression	1
Triclosan	increases expression	1

Clinical trials (associated diseases)

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