DCDC2B

Summary

DCDC2B (doublecortin domain containing 2B, HGNC:32576) is a protein-coding gene on chromosome 1p35.2, encoding Doublecortin domain-containing protein 2B (A2VCK2).

This gene encodes a member of the doublecortin family. The protein encoded by this gene contains two doublecortin domains. The doublecortin domain has been demonstrated to bind tubulin and enhance microtubule polymerization.

Source: NCBI Gene 149069 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 64 total
• MANE Select transcript: NM_001099434

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32576
Approved symbol	DCDC2B
Name	doublecortin domain containing 2B
Location	1p35.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000222046
Ensembl biotype	protein_coding
Entrez	149069

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000409358, ENST00000487056, ENST00000906474

RefSeq mRNA: 1 — MANE Select: NM_001099434 NM_001099434

CCDS: CCDS44100

Canonical transcript exons

ENST00000409358 — 9 exons

Exon	Start	End
ENSE00001579528	32215802	32216192
ENSE00001583558	32212490	32212636
ENSE00001587965	32209089	32209359
ENSE00001588833	32212070	32212201
ENSE00001589585	32211761	32211837
ENSE00003610385	32212754	32212793
ENSE00003632400	32211272	32211323
ENSE00003663174	32214797	32214932
ENSE00003686934	32215440	32215543

Expression profiles

Bgee: expression breadth ubiquitous, 157 present calls, max score 97.22.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0450 / max 18.5515, expressed in 17 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
1961	0.0450	17

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	97.22	gold quality
bronchial epithelial cell	CL:0002328	90.84	gold quality
bronchus	UBERON:0002185	90.14	gold quality
nasal cavity epithelium	UBERON:0005384	89.12	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	86.94	gold quality
kidney epithelium	UBERON:0004819	86.67	gold quality
upper arm skin	UBERON:0004263	82.68	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	81.23	gold quality
epithelial cell of pancreas	CL:0000083	81.01	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.72	silver quality
vena cava	UBERON:0004087	80.48	silver quality
cerebellar vermis	UBERON:0004720	79.36	silver quality
nasal cavity mucosa	UBERON:0001826	78.89	gold quality
heart right ventricle	UBERON:0002080	78.67	gold quality
vastus lateralis	UBERON:0001379	78.18	gold quality
quadriceps femoris	UBERON:0001377	78.09	gold quality
substantia nigra pars compacta	UBERON:0001965	78.05	silver quality
lateral globus pallidus	UBERON:0002476	77.85	silver quality
fallopian tube	UBERON:0003889	77.74	gold quality
sperm	CL:0000019	77.67	gold quality
lateral nuclear group of thalamus	UBERON:0002736	77.65	gold quality
subthalamic nucleus	UBERON:0001906	77.49	silver quality
pharyngeal mucosa	UBERON:0000355	77.21	gold quality
pons	UBERON:0000988	76.78	silver quality
dorsal plus ventral thalamus	UBERON:0001897	76.54	silver quality
mucosa of paranasal sinus	UBERON:0005030	76.48	gold quality
cardiac muscle of right atrium	UBERON:0003379	76.14	gold quality
left ventricle myocardium	UBERON:0006566	76.03	gold quality
cardia of stomach	UBERON:0001162	76.01	silver quality
body of tongue	UBERON:0011876	75.93	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.87

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting DCDC2B, 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-6793-5P	99.97	65.95	758
HSA-MIR-8080	99.82	67.52	1342
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-5580-5P	99.38	66.96	1139
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-3190-5P	98.87	64.89	1345
HSA-MIR-6829-5P	98.86	65.12	1480
HSA-MIR-3194-3P	98.83	66.22	1167
HSA-MIR-629-5P	98.78	68.72	1032
HSA-MIR-767-3P	98.61	67.69	1192
HSA-MIR-6847-5P	97.93	66.74	1808
HSA-MIR-4446-3P	97.91	64.29	991
HSA-MIR-630	97.50	66.38	921
HSA-MIR-4435	95.90	65.47	1201
HSA-MIR-3943	95.87	64.57	523

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Dcdc2b	ENSMUSG00000078552

Paralogs (2): DCDC2 (ENSG00000146038), DCDC2C (ENSG00000214866)

Protein

Protein identifiers

Doublecortin domain-containing protein 2B — A2VCK2 (reviewed: A2VCK2)

All UniProt accessions (1): A2VCK2

RefSeq proteins (1): NP_001092904* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003533	Doublecortin_dom	Domain
IPR036572	Doublecortin_dom_sf	Homologous_superfamily

Pfam: PF03607

UniProt features (6 total): domain 2, region of interest 2, chain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A2VCK2-F1	68.12	0.12

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 36 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, GOCC_MICROTUBULE_ORGANIZING_CENTER, chr1p35, DODD_NASOPHARYNGEAL_CARCINOMA_DN, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, GOCC_SUPRAMOLECULAR_POLYMER, ZNF30_TARGET_GENES, ZNF8_TARGET_GENES, GSE10239_NAIVE_VS_KLRG1INT_EFF_CD8_TCELL_UP, GSE10239_NAIVE_VS_KLRG1HIGH_EFF_CD8_TCELL_UP, GSE10239_NAIVE_VS_DAY4.5_EFF_CD8_TCELL_UP, MIR8080, GSE13229_IMM_VS_INTMATURE_NKCELL_UP, DESCARTES_MAIN_FETAL_CILIATED_EPITHELIAL_CELLS

GO Biological Process (1): intracellular signal transduction (GO:0035556)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): microtubule organizing center (GO:0005815), microtubule (GO:0005874)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
microtubule cytoskeleton	2
intracellular anatomical structure	1
signal transduction	1
binding	1
cellular anatomical structure	1
polymeric cytoskeletal fiber	1

Protein interactions and networks

STRING

447 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DCDC2B	DNAAF4	Q8WXU2	637
DCDC2B	KIAA0319	Q5VV43	578
DCDC2B	CCDC87	Q9NVE4	561
DCDC2B	KLHL23	Q8NBE8	478
DCDC2B	ATP2C2	O75185	474
DCDC2B	CMIP	Q8IY22	460
DCDC2B	MFSD6L	Q8IWD5	444
DCDC2B	NAGPA	Q9UK23	423
DCDC2B	SLC15A5	A6NIM6	414
DCDC2B	SLC35F5	Q8WV83	408
DCDC2B	GNPTG	Q9UJJ9	397
DCDC2B	FMR1	Q06787	395
DCDC2B	MIX23	Q4VC31	389
DCDC2B	POT1	Q9NUX5	383
DCDC2B	GNPTAB	Q3T906	378

IntAct

40 interactions, top by confidence:

A	B	Type	Score
DCDC2B	FHL3	psi-mi:“MI:0915”(physical association)	0.720
FHL3	DCDC2B	psi-mi:“MI:0915”(physical association)	0.720
DCDC2B	MTUS2	psi-mi:“MI:0915”(physical association)	0.560
KRT40	DCDC2B	psi-mi:“MI:0915”(physical association)	0.560
BANP	DCDC2B	psi-mi:“MI:0915”(physical association)	0.560
RBPMS	DCDC2B	psi-mi:“MI:0915”(physical association)	0.560
MTUS2	DCDC2B	psi-mi:“MI:0915”(physical association)	0.560
DCDC2B	BANP	psi-mi:“MI:0915”(physical association)	0.560
DCDC2B	RBPMS	psi-mi:“MI:0915”(physical association)	0.560
DCDC2B	CYSRT1	psi-mi:“MI:0915”(physical association)	0.560
DCDC2B	HSF2BP	psi-mi:“MI:0915”(physical association)	0.560
DCDC2B	KRTAP3-3	psi-mi:“MI:0915”(physical association)	0.560
DCDC2B	ZNF574	psi-mi:“MI:0915”(physical association)	0.560
DCDC2B	FHL5	psi-mi:“MI:0915”(physical association)	0.560
DCDC2B	FRS3	psi-mi:“MI:0915”(physical association)	0.560
DCDC2B	HSPA8	psi-mi:“MI:0914”(association)	0.530
DCDC2B	HMGN1	psi-mi:“MI:0915”(physical association)	0.400
DCDC2B	HSF2BP	psi-mi:“MI:0915”(physical association)	0.000
DCDC2B	CYSRT1	psi-mi:“MI:0915”(physical association)	0.000
DCDC2B	FHL3	psi-mi:“MI:0915”(physical association)	0.000
DCDC2B	KRTAP3-3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (28): DCDC2B (Two-hybrid), DCDC2B (Two-hybrid), DCDC2B (Two-hybrid), DCDC2B (Two-hybrid), DCDC2B (Two-hybrid), FAT3 (Affinity Capture-MS), FAT4 (Affinity Capture-MS), PSMG4 (Affinity Capture-MS), FHL2 (Affinity Capture-MS), HSPA8 (Affinity Capture-MS), PSMG3 (Affinity Capture-MS), PCDH20 (Affinity Capture-MS), DCDC2B (Two-hybrid), DCDC2B (Two-hybrid), DCDC2B (Two-hybrid)

ESM2 similar proteins: A1L3T7, A2CI98, A2CJ06, A2VCK2, D3ZQL6, E1BBG2, M3WHG5, O15037, O43918, O70303, O75333, P48778, P59729, Q32PJ7, Q3KP66, Q3T191, Q5JYT7, Q5T124, Q5U4F0, Q5XIS1, Q6AXX1, Q6VYH9, Q7TSI1, Q80U38, Q8BGT6, Q8BHW9, Q8BWG4, Q8BWQ5, Q8BZ33, Q8BZW2, Q8C0J6, Q8C2K5, Q8CFK6, Q8IV53, Q8IY33, Q8IZW8, Q8K1S6, Q8K330, Q8N3F8, Q8TB24

Diamond homologs: A2VCK2, A8MYV0, D3ZR10, Q5DU00, Q9D1B8, Q9UHG0, Q9VUI3, P56715, P56716, Q550F6, Q69Z08, Q8CGM2, Q8IWN7, Q8MJ03, Q8MJ04, Q8MJ05, Q8MJ06, D2I3C6, O15075, O43602, O88809, Q5MPA9, Q6PGN3, Q8N568, Q95QC4, Q9JLM8, Q9ESI7, O00423, O95834, Q05BC3, Q26613, Q2TAF3, Q32P44, Q3UMY5, Q4V8C3, Q6DIP5, Q6P6T4, Q7TNG5, Q8VC03, Q9HC35

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	54
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1675 predictions. Top by Δscore:

Variant	Effect	Δscore
1:32209316:GGGCA:G	donor_gain	1.0000
1:32209317:GGCAG:G	donor_gain	1.0000
1:32209318:G:T	donor_gain	1.0000
1:32209321:G:GG	donor_gain	1.0000
1:32209360:G:GG	donor_gain	1.0000
1:32211324:G:GG	donor_gain	1.0000
1:32215435:TTTA:T	acceptor_loss	1.0000
1:32215437:TA:T	acceptor_loss	1.0000
1:32215438:A:AC	acceptor_loss	1.0000
1:32215438:A:AG	acceptor_gain	1.0000
1:32215439:G:GG	acceptor_gain	1.0000
1:32209397:G:T	donor_gain	0.9900
1:32211270:A:AG	acceptor_gain	0.9900
1:32211271:G:GG	acceptor_gain	0.9900
1:32211271:GCT:G	acceptor_gain	0.9900
1:32212487:CAG:C	acceptor_loss	0.9900
1:32212487:CAGA:C	acceptor_gain	0.9900
1:32212488:A:AG	acceptor_gain	0.9900
1:32212489:G:GG	acceptor_gain	0.9900
1:32212489:GA:G	acceptor_gain	0.9900
1:32212489:GACTC:G	acceptor_gain	0.9900
1:32212569:GA:G	donor_gain	0.9900
1:32215438:AG:A	acceptor_gain	0.9900
1:32215439:GG:G	acceptor_gain	0.9900
1:32215439:GGA:G	acceptor_gain	0.9900
1:32215439:GGAGT:G	acceptor_gain	0.9900
1:32209317:GGCA:G	donor_gain	0.9800
1:32209318:GCAG:G	donor_gain	0.9800
1:32209356:TCCA:T	donor_gain	0.9800
1:32212069:GT:G	acceptor_gain	0.9800

AlphaMissense

2223 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:32212074:T:C	F134L	0.964
1:32212076:C:A	F134L	0.964
1:32212076:C:G	F134L	0.964
1:32212558:C:A	A199D	0.953
1:32209190:T:C	F33L	0.949
1:32209192:C:A	F33L	0.949
1:32209192:C:G	F33L	0.949
1:32209305:T:C	L71S	0.945
1:32212072:T:A	V133E	0.937
1:32212075:T:C	F134S	0.935
1:32212575:T:C	F205L	0.930
1:32212577:C:A	F205L	0.930
1:32212577:C:G	F205L	0.930
1:32209329:C:A	A79D	0.924
1:32212082:T:A	N136K	0.924
1:32212082:T:G	N136K	0.924
1:32212081:A:T	N136I	0.920
1:32209322:T:C	Y77H	0.916
1:32212492:T:A	L177H	0.912
1:32209209:T:C	F39S	0.911
1:32209346:T:C	F85L	0.909
1:32209348:C:A	F85L	0.909
1:32209348:C:G	F85L	0.909
1:32209323:A:C	Y77S	0.903
1:32212555:T:A	V198E	0.902
1:32212551:T:G	Y197D	0.899
1:32209322:T:G	Y77D	0.897
1:32209287:T:A	V65D	0.894
1:32212084:G:T	G137V	0.883
1:32209141:T:A	N16K	0.873

dbSNP variants (sampled 300 via entrez): RS1000506821 (1:32208946 A>G), RS1000713531 (1:32216362 T>C), RS1000992739 (1:32209678 C>A,G), RS1001072443 (1:32213878 A>G), RS1001149018 (1:32211587 G>C), RS1001210066 (1:32211278 A>C,G), RS1002479267 (1:32215275 G>A,C), RS1002640719 (1:32211968 A>G,T), RS1003287179 (1:32213802 G>A), RS1003294999 (1:32212399 C>T), RS1003524935 (1:32212391 G>A,C), RS1003732344 (1:32207097 C>T), RS1004169343 (1:32215158 GC>G,GCC), RS1004403098 (1:32209966 G>A), RS1004502278 (1:32213785 C>T)

Disease associations

OMIM: gene `` | 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

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
butyraldehyde	increases expression	1
jinfukang	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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