BICDL2

Summary

BICDL2 (BICD family like cargo adaptor 2, HGNC:33584) is a protein-coding gene on chromosome 16p13.3, encoding BICD family-like cargo adapter 2 (A1A5D9).

Predicted to enable small GTPase binding activity. Predicted to be involved in Golgi to secretory granule transport and vesicle transport along microtubule. Predicted to be located in cytoplasm.

Source: NCBI Gene 146439 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 24 total — 2 pathogenic
• MANE Select transcript: NM_001369667

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33584
Approved symbol	BICDL2
Name	BICD family like cargo adaptor 2
Location	16p13.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000162069
Ensembl biotype	protein_coding
OMIM	617003
Entrez	146439

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 13 protein_coding, 2 retained_intron

ENST00000389347, ENST00000572240, ENST00000572449, ENST00000573514, ENST00000576826, ENST00000642419, ENST00000873753, ENST00000873754, ENST00000873755, ENST00000873756, ENST00000873757, ENST00000873758, ENST00000915135, ENST00000957824, ENST00000957825

RefSeq mRNA: 2 — MANE Select: NM_001369667 NM_001103175, NM_001369667

CCDS: CCDS45393

Canonical transcript exons

ENST00000572449 — 10 exons

Exon	Start	End
ENSE00001505609	3029545	3029739
ENSE00003490279	3030935	3031150
ENSE00003547680	3030696	3030812
ENSE00003553190	3028700	3028830
ENSE00003568461	3029280	3029429
ENSE00003572109	3035215	3035526
ENSE00003633887	3030449	3030595
ENSE00003688891	3028348	3028468
ENSE00003888875	3036894	3036944
ENSE00003894474	3027682	3028273

Expression profiles

Bgee: expression breadth ubiquitous, 180 present calls, max score 98.52.

FANTOM5 (CAGE): breadth broad, TPM avg 0.9435 / max 54.2742, expressed in 337 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
155993	0.5929	250
155990	0.1899	95
155991	0.1308	54
155992	0.0298	23

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	98.52	gold quality
lower esophagus mucosa	UBERON:0035834	98.52	gold quality
body of pancreas	UBERON:0001150	97.97	gold quality
mucosa of transverse colon	UBERON:0004991	96.20	gold quality
esophagus mucosa	UBERON:0002469	96.16	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.81	gold quality
minor salivary gland	UBERON:0001830	93.66	gold quality
skin of abdomen	UBERON:0001416	93.25	gold quality
nasal cavity epithelium	UBERON:0005384	93.11	gold quality
skin of leg	UBERON:0001511	92.20	gold quality
mouth mucosa	UBERON:0003729	92.10	gold quality
saliva-secreting gland	UBERON:0001044	91.12	gold quality
right uterine tube	UBERON:0001302	90.23	gold quality
zone of skin	UBERON:0000014	89.22	gold quality
ileal mucosa	UBERON:0000331	86.28	gold quality
pancreas	UBERON:0001264	85.52	gold quality
upper arm skin	UBERON:0004263	85.37	silver quality
buccal mucosa cell	CL:0002336	85.35	gold quality
transverse colon	UBERON:0001157	85.32	gold quality
vagina	UBERON:0000996	84.28	gold quality
nasal cavity mucosa	UBERON:0001826	84.23	gold quality
esophagus squamous epithelium	UBERON:0006920	83.97	gold quality
parotid gland	UBERON:0001831	83.64	gold quality
body of stomach	UBERON:0001161	82.70	gold quality
small intestine Peyer’s patch	UBERON:0003454	80.46	gold quality
pharyngeal mucosa	UBERON:0000355	80.28	gold quality
prostate gland	UBERON:0002367	80.18	gold quality
oral cavity	UBERON:0000167	80.01	gold quality
palpebral conjunctiva	UBERON:0001812	79.46	gold quality
stomach	UBERON:0000945	79.32	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-114	yes	56.11
E-ANND-3	yes	9.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting BICDL2, 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-6077	99.99	68.04	2299
HSA-MIR-6079	99.84	68.54	1170
HSA-MIR-7-5P	99.67	70.53	1809
HSA-MIR-4758-3P	99.12	63.96	869
HSA-MIR-1225-3P	97.29	64.60	876
HSA-MIR-1913	97.07	66.20	1417
HSA-MIR-1233-3P	96.81	65.44	573
HSA-MIR-6769A-3P	94.91	61.36	412

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	bicdl2	ENSDARG00000052427
mus_musculus	Bicdl2	ENSMUSG00000043782
rattus_norvegicus	Bicdl2	ENSRNOG00000003457
drosophila_melanogaster	CG32137	FBGN0052137

Paralogs (2): SPDL1 (ENSG00000040275), BICDL1 (ENSG00000135127)

Protein

Protein identifiers

BICD family-like cargo adapter 2 — A1A5D9 (reviewed: A1A5D9)

Alternative names: Bicaudal D-related protein 2, Coiled-coil domain-containing protein 64B

All UniProt accessions (2): A0A2R8Y2X6, A1A5D9

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with RAB13.

Similarity. Belongs to the BICDR family.

Isoforms (2)

UniProt ID	Names	Canonical?
A1A5D9-1	1	yes
A1A5D9-2	2

RefSeq proteins (2): NP_001096645, NP_001356596* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR051149	Spindly/BICDR_Dynein_Adapter	Family

UniProt features (13 total): region of interest 4, compositionally biased region 3, sequence variant 2, coiled-coil region 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A1A5D9-F1	80.99	0.63

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 52 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, GOBP_VESICLE_LOCALIZATION, GOBP_ORGANELLE_TRANSPORT_ALONG_MICROTUBULE, GOMF_GTPASE_BINDING, GOBP_VESICLE_CYTOSKELETAL_TRAFFICKING, GOBP_ORGANELLE_LOCALIZATION, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP, LIU_LIVER_CANCER, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MIKKELSEN_MEF_ICP_WITH_H3K27ME3, MIKKELSEN_IPS_ICP_WITH_H3K4ME3_AND_H327ME3, DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN, GOBP_INTRACELLULAR_TRANSPORT, GOBP_ESTABLISHMENT_OF_ORGANELLE_LOCALIZATION, GOBP_MICROTUBULE_BASED_TRANSPORT

GO Biological Process (2): vesicle transport along microtubule (GO:0047496), Golgi to secretory granule transport (GO:0055107)

GO Molecular Function (2): small GTPase binding (GO:0031267), protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
organelle transport along microtubule	1
vesicle cytoskeletal trafficking	1
intercellular transport	1
intracellular transport	1
GTPase binding	1
binding	1

Protein interactions and networks

STRING

456 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BICDL2	BICD2	Q8TD16	622
BICDL2	BICD1	Q96G01	603
BICDL2	CCDC78	A2IDD5	589
BICDL2	RAB13	P51153	560
BICDL2	HOOK2	Q96ED9	544
BICDL2	C20orf204	A0A1B0GTL2	543
BICDL2	HOOK3	Q86VS8	540
BICDL2	HOOK1	Q9UJC3	501
BICDL2	RAB11FIP3	O75154	500
BICDL2	FLYWCH2	Q96CP2	487
BICDL2	CRACR2A	Q9BSW2	466
BICDL2	RASEF	Q8IZ41	460
BICDL2	HCFC1R1	Q9NWW0	456
BICDL2	NINL	Q9Y2I6	448
BICDL2	TMEM235	A6NFC5	432

IntAct

34 interactions, top by confidence:

A	B	Type	Score
BICDL2	KLC3	psi-mi:“MI:0915”(physical association)	0.670
KLC3	BICDL2	psi-mi:“MI:0915”(physical association)	0.670
	BICDL2	psi-mi:“MI:0915”(physical association)	0.560
BICDL2		psi-mi:“MI:0915”(physical association)	0.560
BICDL2	API5	psi-mi:“MI:0915”(physical association)	0.560
BICDL2	RPL9	psi-mi:“MI:0915”(physical association)	0.560
BICDL2	KLC3	psi-mi:“MI:0915”(physical association)	0.560
BICDL2	TSGA10IP	psi-mi:“MI:0915”(physical association)	0.560
BICDL2	PKP1	psi-mi:“MI:0915”(physical association)	0.560
BICDL2	CDK17	psi-mi:“MI:0915”(physical association)	0.560
BICDL2		psi-mi:“MI:0915”(physical association)	0.370
BICDL2	S	psi-mi:“MI:0915”(physical association)	0.370
BICDL2	CFTR	psi-mi:“MI:0915”(physical association)	0.370
CFTR	BICDL2	psi-mi:“MI:0915”(physical association)	0.370
SYNC	BICDL2	psi-mi:“MI:0914”(association)	0.350
CARD9	BICDL2	psi-mi:“MI:0914”(association)	0.350
API5	BICDL2	psi-mi:“MI:0915”(physical association)	0.000
RPL9	BICDL2	psi-mi:“MI:0915”(physical association)	0.000
KLC3	BICDL2	psi-mi:“MI:0915”(physical association)	0.000
PKP1	BICDL2	psi-mi:“MI:0915”(physical association)	0.000
TSGA10IP	BICDL2	psi-mi:“MI:0915”(physical association)	0.000
CDK17	BICDL2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (14): KLC3 (Two-hybrid), CCDC64B (Two-hybrid), CCDC64B (Two-hybrid), CCDC64B (Two-hybrid), RPL9 (Two-hybrid), API5 (Two-hybrid), TSGA10IP (Two-hybrid), CCDC64B (Affinity Capture-MS), CCDC64B (Affinity Capture-MS), CCDC64B (Two-hybrid), CCDC64B (Two-hybrid), CCDC64B (Two-hybrid), CCDC64B (PCA), CCDC64B (Affinity Capture-MS)

ESM2 similar proteins: A0A140LIT1, A0A1B0GVG4, A0JNH6, A1A5D9, A6NC98, A6NGB0, A6NJZ7, A6NNM3, F6XLV1, O15049, O54887, P0C7N4, P58660, P60531, Q0D2H9, Q0P5D1, Q2KJ21, Q2TAC2, Q3LUD3, Q3T1I3, Q3TMW1, Q3V0F0, Q4QRL3, Q5JTB6, Q5RD60, Q66HR5, Q6NSJ2, Q6PHN1, Q6QZQ4, Q80VM7, Q8BP01, Q8C7U1, Q8CB62, Q8CGU1, Q8CHW5, Q8K2I2, Q8N137, Q8N283, Q8N6Y0, Q8R370

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	7
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
253470	GRCh37/hg19 16p13.3(chr16:2867891-3942436)x3	Pathogenic
2684774	GRCh37/hg19 16p13.3(chr16:2606711-3935836)x3	Pathogenic

SpliceAI

2011 predictions. Top by Δscore:

Variant	Effect	Δscore
16:3028344:TCA:T	donor_loss	1.0000
16:3028345:CACC:C	donor_loss	1.0000
16:3028464:GGGCC:G	acceptor_gain	1.0000
16:3028466:GCC:G	acceptor_gain	1.0000
16:3028467:CC:C	acceptor_gain	1.0000
16:3028467:CCC:C	acceptor_gain	1.0000
16:3028468:CC:C	acceptor_gain	1.0000
16:3028468:CCTAG:C	acceptor_loss	1.0000
16:3028469:C:CC	acceptor_gain	1.0000
16:3028469:CTAGG:C	acceptor_loss	1.0000
16:3028470:T:G	acceptor_loss	1.0000
16:3028474:C:CT	acceptor_gain	1.0000
16:3028475:G:T	acceptor_gain	1.0000
16:3028478:C:CT	acceptor_gain	1.0000
16:3028694:GCTTA:G	donor_loss	1.0000
16:3028695:CTTA:C	donor_loss	1.0000
16:3028696:TTACT:T	donor_loss	1.0000
16:3028697:TACTT:T	donor_loss	1.0000
16:3028698:A:AC	donor_gain	1.0000
16:3028698:ACT:A	donor_loss	1.0000
16:3028699:C:CT	donor_gain	1.0000
16:3028699:CT:C	donor_gain	1.0000
16:3028699:CTT:C	donor_gain	1.0000
16:3028699:CTTG:C	donor_gain	1.0000
16:3028699:CTTGT:C	donor_gain	1.0000
16:3028700:TTGTT:T	donor_gain	1.0000
16:3028701:TGTTC:T	donor_gain	1.0000
16:3028757:T:TA	donor_gain	1.0000
16:3028826:GAGAT:G	acceptor_gain	1.0000
16:3028827:AGAT:A	acceptor_gain	1.0000

AlphaMissense

3197 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:3028353:A:G	W452R	0.996
16:3028353:A:T	W452R	0.996
16:3028351:C:A	W452C	0.994
16:3028351:C:G	W452C	0.994
16:3028361:A:G	L449P	0.994
16:3028403:A:G	L435P	0.992
16:3028356:C:G	A451P	0.989
16:3028373:A:G	L445P	0.987
16:3035294:C:T	G68D	0.987
16:3035304:C:G	A65P	0.987
16:3028349:T:G	Q453P	0.984
16:3035295:C:G	G68R	0.982
16:3035285:A:G	L71P	0.981
16:3035315:A:G	L61P	0.981
16:3028269:T:A	D455V	0.980
16:3035294:C:A	G68V	0.979
16:3028352:C:G	W452S	0.978
16:3028269:T:G	D455A	0.977
16:3028254:A:T	I460N	0.976
16:3030812:C:G	A167P	0.972
16:3030954:A:G	L160P	0.972
16:3035297:A:G	L67P	0.972
16:3035306:G:T	A64D	0.972
16:3028381:C:A	K442N	0.971
16:3028381:C:G	K442N	0.971
16:3028395:C:G	A438P	0.970
16:3028270:C:G	D455H	0.969
16:3028377:C:G	A444P	0.967
16:3028268:G:C	D455E	0.966
16:3028268:G:T	D455E	0.966

dbSNP variants (sampled 300 via entrez): RS1000024355 (16:3036078 C>T), RS1000028770 (16:3032511 C>T), RS1000308899 (16:3036969 C>T), RS1000447187 (16:3032401 C>A,G,T), RS1000525687 (16:3036757 GCCGGCGCCCCCGGTTCC>G), RS1000613828 (16:3028751 G>A,C), RS1000614794 (16:3037081 C>T), RS1000733136 (16:3033425 G>A), RS1000785412 (16:3033753 C>A), RS1001137490 (16:3037767 G>C), RS1001188656 (16:3032124 G>A,T), RS1001291884 (16:3032779 T>C,G), RS1001420158 (16:3037505 G>A), RS1001728763 (16:3027815 G>C,T), RS1001777650 (16:3028063 G>A)

Disease associations

OMIM: gene MIM:617003 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, increases methylation, affects cotreatment	3
sodium arsenite	decreases expression, increases expression	2
Tobacco Smoke Pollution	increases expression, decreases expression	2
aristolochic acid I	increases expression	1
sotorasib	affects cotreatment, increases expression	1
aminomethylphosphonic acid (AMPA)	decreases expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
ethyl-p-hydroxybenzoate	increases expression	1
ferrous chloride	decreases expression	1
fipronil	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
licochalcone B	increases expression	1
jinfukang	decreases expression, affects cotreatment	1
trametinib	affects cotreatment, increases expression	1
NVP-BKM120	affects cotreatment, increases expression	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation	1
Cisplatin	affects cotreatment, decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Melphalan	increases expression	1
Ozone	affects expression, increases abundance	1
Smoke	decreases expression	1
2,4-Dichlorophenoxyacetic Acid	decreases expression	1
Cadmium Chloride	increases expression	1
Particulate Matter	decreases expression	1

Clinical trials (associated diseases)

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