CNTNAP3B

Summary

CNTNAP3B (contactin associated protein family member 3B, HGNC:32035) is a protein-coding gene on chromosome 9p11.2, encoding Contactin-associated protein-like 3B (Q96NU0).

Predicted to be involved in cell adhesion. Predicted to be located in membrane.

Source: NCBI Gene 728577 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 338 total
• MANE Select transcript: NM_001201380

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32035
Approved symbol	CNTNAP3B
Name	contactin associated protein family member 3B
Location	9p11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000154529
Ensembl biotype	protein_coding
Entrez	728577

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 14 protein_coding, 3 retained_intron, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000276974, ENST00000341990, ENST00000377561, ENST00000467854, ENST00000476961, ENST00000479351, ENST00000480466, ENST00000484254, ENST00000489789, ENST00000491438, ENST00000612828, ENST00000617422, ENST00000617848, ENST00000618777, ENST00000619138, ENST00000902379, ENST00000902380, ENST00000955695, ENST00000955696, ENST00000955697, ENST00000955698, ENST00000955699

RefSeq mRNA: 1 — MANE Select: NM_001201380 NM_001201380

CCDS: CCDS75836

Canonical transcript exons

ENST00000377561 — 24 exons

Exon	Start	End
ENSE00001844388	42129010	42129426
ENSE00001851404	41890536	41894110
ENSE00001951240	41898462	41898533
ENSE00003458509	41906854	41906987
ENSE00003460696	41970074	41970245
ENSE00003464782	42076869	42077062
ENSE00003468443	41922677	41922895
ENSE00003470578	41923923	41924093
ENSE00003488902	41908557	41908781
ENSE00003522083	41991610	41991871
ENSE00003526345	41929317	41929444
ENSE00003530177	41960773	41960892
ENSE00003533263	41998401	41998604
ENSE00003539483	41986168	41986311
ENSE00003549045	42104629	42104739
ENSE00003556489	41920070	41920309
ENSE00003596889	42013378	42013525
ENSE00003630541	41953183	41953386
ENSE00003641432	41996205	41996348
ENSE00003669769	41964538	41964644
ENSE00003673980	41997568	41997752
ENSE00003676979	41938244	41938400
ENSE00003746936	41898769	41898999
ENSE00003751338	41905868	41905955

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 95.57.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of stomach	UBERON:0001199	95.57	gold quality
lower esophagus muscularis layer	UBERON:0035833	93.36	gold quality
lower esophagus	UBERON:0013473	93.33	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	91.39	gold quality
quadriceps femoris	UBERON:0001377	91.13	gold quality
thoracic mammary gland	UBERON:0005200	88.96	gold quality
cerebellar vermis	UBERON:0004720	88.59	gold quality
esophagus	UBERON:0001043	87.91	gold quality
ventricular zone	UBERON:0003053	87.60	gold quality
subcutaneous adipose tissue	UBERON:0002190	87.05	gold quality
skin of abdomen	UBERON:0001416	86.61	gold quality
adipose tissue	UBERON:0001013	86.50	gold quality
muscle layer of sigmoid colon	UBERON:0035805	86.45	gold quality
omental fat pad	UBERON:0010414	86.04	gold quality
zone of skin	UBERON:0000014	85.99	gold quality
skin of leg	UBERON:0001511	85.58	gold quality
minor salivary gland	UBERON:0001830	85.16	gold quality
nucleus accumbens	UBERON:0001882	84.99	gold quality
sural nerve	UBERON:0015488	83.94	gold quality
saliva-secreting gland	UBERON:0001044	83.91	gold quality
right atrium auricular region	UBERON:0006631	83.91	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.51	gold quality
esophagus mucosa	UBERON:0002469	82.90	gold quality
thymus	UBERON:0002370	82.75	silver quality
right uterine tube	UBERON:0001302	82.71	gold quality
calcaneal tendon	UBERON:0003701	82.61	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.54	gold quality
lower esophagus mucosa	UBERON:0035834	82.48	gold quality
caudate nucleus	UBERON:0001873	82.27	gold quality
descending thoracic aorta	UBERON:0002345	81.96	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	45.72
E-CURD-112	yes	11.55
E-ANND-3	yes	6.36
E-MTAB-10137	no	219.12

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

124 targeting CNTNAP3B, 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-4262	100.00	73.26	3931
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-454-3P	99.91	74.01	1925

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cntnap3	ENSDARG00000067824
mus_musculus	Cntnap3	ENSMUSG00000033063
rattus_norvegicus	Cntnap3	ENSRNOG00000027309

Paralogs (35): NRXN3 (ENSG00000021645), TLL1 (ENSG00000038295), CP (ENSG00000047457), DCBLD2 (ENSG00000057019), HEPH (ENSG00000089472), TLL2 (ENSG00000095587), NRP1 (ENSG00000099250), PCOLCE (ENSG00000106333), CNTNAP3 (ENSG00000106714), CUBN (ENSG00000107611), CNTNAP1 (ENSG00000108797), NRXN2 (ENSG00000110076), MEP1A (ENSG00000112818), NRP2 (ENSG00000118257), CUZD1 (ENSG00000138161), MFGE8 (ENSG00000140545), MEP1B (ENSG00000141434), PDGFC (ENSG00000145431), CNTNAP4 (ENSG00000152910), CNTNAP5 (ENSG00000155052), CDCP2 (ENSG00000157211), PCOLCE2 (ENSG00000163710), EDIL3 (ENSG00000164176), NETO1 (ENSG00000166342), BMP1 (ENSG00000168487), PDGFD (ENSG00000170962), NETO2 (ENSG00000171208), CNTNAP2 (ENSG00000174469), NRXN1 (ENSG00000179915), HEPHL1 (ENSG00000181333), F8 (ENSG00000185010), ASTL (ENSG00000188886), F5 (ENSG00000198734), MFRP (ENSG00000235718), CNTNAP3C (ENSG00000283378)

Protein

Protein identifiers

Contactin-associated protein-like 3B — Q96NU0 (reviewed: Q96NU0)

Alternative names: Cell recognition molecule Caspr3b

All UniProt accessions (9): Q96NU0, A0A087WUG9, A0A087WXL9, A0A087WZ03, A0A087X0T4, A0A087X119, A0A087X2E4, A0A2P0CT92, F2Z2X5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Miscellaneous. The gene encoding CNTNAP3B is the result of a pericentromeric duplication of the genomic region encoding CNTNAP3 on chromosome 9. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the neurexin family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96NU0-1	1	yes
Q96NU0-2	2

RefSeq proteins (1): NP_001188309* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000421	FA58C	Domain
IPR000742	EGF	Domain
IPR001791	Laminin_G	Domain
IPR002181	Fibrinogen_a/b/g_C_dom	Domain
IPR008979	Galactose-bd-like_sf	Homologous_superfamily
IPR013320	ConA-like_dom_sf	Homologous_superfamily
IPR036056	Fibrinogen-like_C	Homologous_superfamily
IPR050372	Neurexin-related_CASP	Family

Pfam: PF00008, PF00754, PF02210

UniProt features (44 total): disulfide bond 11, sequence conflict 11, domain 8, splice variant 4, region of interest 2, glycosylation site 2, topological domain 2, signal peptide 1, chain 1, compositionally biased region 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96NU0-F1	83.51	0.57

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (11): 31–177, 332–364, 513–545, 551–562, 556–571, 573–583, 931–958, 962–975, 969–984, 986–996, 1167–1203

Glycosylation sites (2): 359, 706

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 71 (showing top): chr9p11, GOCC_SYNAPSE, NUYTTEN_NIPP1_TARGETS_DN, PURBEY_TARGETS_OF_CTBP1_AND_SATB1_DN, IL15_UP.V1_DN, IL21_UP.V1_DN, HMGA1_TARGET_GENES, MIR153_5P, MIR4262, MIR3671, MIR1297, MIR3680_3P, MIR1305, MIR4422, MIR548F_5P

GO Biological Process (1): cell adhesion (GO:0007155)

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular process	1
cellular anatomical structure	1

Protein interactions and networks

STRING

334 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CNTNAP3B	SPATA31A3	Q5VYP0	621
CNTNAP3B	PHF24	Q9UPV7	419
CNTNAP3B	CCDC144NL	Q6NUI1	407
CNTNAP3B	NBPF9	P0DPF3	376
CNTNAP3B	ZNG1C	Q5JTY5	370
CNTNAP3B	ZNG1E	Q5RIA9	370
CNTNAP3B	ZXDB	P98169	368
CNTNAP3B	VSIG10L	Q86VR7	366
CNTNAP3B	BABAM1	Q9NWV8	353
CNTNAP3B	CREB5	Q02930	351
CNTNAP3B	UNKL	Q9H9P5	349
CNTNAP3B	KRTAP5-11	Q6L8G4	348
CNTNAP3B	KRTAP5-5	Q701N2	348
CNTNAP3B	KANK2	Q63ZY3	348
CNTNAP3B	CEACAM8	P31997	342

IntAct

58 interactions, top by confidence:

A	B	Type	Score
C1QTNF9	C1QTNF9B	psi-mi:“MI:0914”(association)	0.780
CD1B	TOR1B	psi-mi:“MI:0914”(association)	0.530
CD1E	SUSD5	psi-mi:“MI:0914”(association)	0.530
GAA	B3GAT3	psi-mi:“MI:0914”(association)	0.530
MMP26	SLC25A20	psi-mi:“MI:0914”(association)	0.530
FBXO2	TMEM131L	psi-mi:“MI:0914”(association)	0.530
CRP	QSOX1	psi-mi:“MI:0914”(association)	0.530
DNAJC3	DEDD	psi-mi:“MI:0914”(association)	0.530
PLAUR	DDX11L8	psi-mi:“MI:0914”(association)	0.350
TMPRSS11B		psi-mi:“MI:0914”(association)	0.350
TMED6	UPK3BL1	psi-mi:“MI:0914”(association)	0.350
PCDH20		psi-mi:“MI:0914”(association)	0.350
TMEM25	FUZ	psi-mi:“MI:0914”(association)	0.350
MMP26	NME4	psi-mi:“MI:0914”(association)	0.350
MPPE1	ADAM10	psi-mi:“MI:0914”(association)	0.350
CCL22	HSPA12A	psi-mi:“MI:0914”(association)	0.350
PON2	ENTPD6	psi-mi:“MI:0914”(association)	0.350
SMPD1	CANX	psi-mi:“MI:0914”(association)	0.350
SHBG	GNB2	psi-mi:“MI:0914”(association)	0.350
	TOR1B	psi-mi:“MI:0914”(association)	0.350
MFAP4	CRLF1	psi-mi:“MI:0914”(association)	0.350
CST9L	QSOX1	psi-mi:“MI:0914”(association)	0.350
CNTNAP3	HSPA5	psi-mi:“MI:0914”(association)	0.350
APOM	ESYT2	psi-mi:“MI:0914”(association)	0.350
BTNL2	TMEM131L	psi-mi:“MI:0914”(association)	0.350
SFTPC	TMEM131L	psi-mi:“MI:0914”(association)	0.350
LY86	TMEM131L	psi-mi:“MI:0914”(association)	0.350

ESM2 similar proteins: A1XQX0, A1XQX2, A1XQX8, A1XQY1, A3KN33, B4F785, B8UU78, D0PRN3, E9Q7X7, M9PE65, P09759, Q02763, Q02858, Q06807, Q07310, Q07497, Q0V8S9, Q0V8T0, Q0V8T3, Q0V8T4, Q0V8T5, Q0V8T6, Q0V8T7, Q0V8T8, Q0V8T9, Q19617, Q28146, Q3KN41, Q4VBE4, Q5RD64, Q63372, Q63374, Q63HQ2, Q6P9K9, Q8CBF3, Q8QFX6, Q8WYK1, Q91571, Q94887, Q96NU0

Diamond homologs: A0EQL2, P04278, P08689, P15196, P97497, Q0V8T5, Q0V8T8, Q62588, Q8WYK1, Q96NU0, Q99P47, A2RUV9, A5A6K7, O14786, O17754, O18806, O35276, O35375, O35474, O43854, O54858, O54991, O60462, O75976, O88783, O89001, P00451, P02886, P02887, P02888, P04836, P12259, P12263, P14384, P15087, P15169, P16870, P21956, P28824, P29068

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 82 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
Metabolism of carbohydrates and carbohydrate derivatives	5	12.0×	7e-03

GO biological processes:

GO term	Partners	Fold	FDR
ERAD pathway	6	14.5×	2e-03
cell adhesion	10	5.0×	5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	301
Likely benign	28
Benign	6

Top pathogenic / likely-pathogenic (0)

SpliceAI

83 predictions. Top by Δscore:

Variant	Effect	Δscore
9:41923891:GG:G	donor_gain	0.9900
9:41923892:GG:G	donor_gain	0.9900
9:41953184:CGAG:C	donor_gain	0.9900
9:41953185:ACGAG:A	donor_gain	0.9500
9:41953031:T:A	acceptor_gain	0.9000
9:41953037:C:A	acceptor_gain	0.8500
9:41923895:ACAGG:A	donor_gain	0.8200
9:41923897:TCACA:T	donor_gain	0.8200
9:41935687:G:GG	acceptor_gain	0.7800
9:41935688:A:AG	acceptor_gain	0.7800
9:41953435:T:A	acceptor_gain	0.7200
9:41965710:G:A	acceptor_gain	0.7000
9:41953432:T:A	acceptor_gain	0.6200
9:41923918:A:T	donor_loss	0.6100
9:41965711:T:TA	acceptor_gain	0.6100
9:41923896:CACAG:C	donor_gain	0.6000
9:41923891:G:C	donor_gain	0.5800
9:41923917:G:GC	donor_loss	0.5500
9:41962808:GC:G	donor_gain	0.5400
9:41923892:G:A	donor_gain	0.5200
9:41923892:GGGT:G	donor_gain	0.5200
9:41923893:AG:A	donor_gain	0.5200
9:41923895:ACAG:A	donor_gain	0.5200
9:41961706:G:T	acceptor_gain	0.5000
9:41953027:T:A	acceptor_gain	0.4800
9:41966681:GA:G	donor_gain	0.4800
9:41923891:GGTA:G	donor_loss	0.4700
9:41923892:GGG:G	donor_loss	0.4700
9:41923916:G:GT	donor_loss	0.4600
9:41962807:C:G	donor_gain	0.4600

AlphaMissense

8361 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:42076976:C:G	A95P	0.998
9:42077051:A:G	W70R	0.998
9:42077051:A:T	W70R	0.998
9:41922804:C:A	W876C	0.997
9:41922804:C:G	W876C	0.997
9:42077049:C:A	W70C	0.996
9:42077049:C:G	W70C	0.996
9:41922806:A:G	W876R	0.995
9:41922806:A:T	W876R	0.995
9:42076978:A:T	V94D	0.995
9:41991747:C:G	R399P	0.994
9:42013404:C:G	R171P	0.994
9:42076899:C:A	W120C	0.994
9:42076899:C:G	W120C	0.994
9:42077017:A:G	L81P	0.994
9:41920281:A:C	F928L	0.993
9:41920281:A:T	F928L	0.993
9:41920282:A:C	F928C	0.993
9:41920283:A:G	F928L	0.993
9:42013511:G:C	N135K	0.993
9:42013511:G:T	N135K	0.993
9:41920282:A:G	F928S	0.992
9:41922803:G:C	H877D	0.992
9:41986286:C:A	W453C	0.992
9:41986286:C:G	W453C	0.992
9:41986288:A:G	W453R	0.992
9:41986288:A:T	W453R	0.992
9:42013389:C:T	G176E	0.992
9:42013449:C:G	R156P	0.992
9:41960784:C:G	C622S	0.991

dbSNP variants (sampled 300 via entrez): RS1000074699 (9:41997953 T>C), RS1000076866 (9:42075696 C>A,T), RS1000080391 (9:42075023 C>A,T), RS1000123757 (9:41984059 A>G), RS1000183125 (9:41949627 G>C), RS1000184808 (9:41997560 A>G), RS1000201665 (9:41918664 A>G,T), RS1000281768 (9:42116301 C>A), RS1000285788 (9:42086950 A>G), RS1000315845 (9:41918254 G>A), RS1000367432 (9:42012334 G>A), RS1000381472 (9:42026796 A>T), RS1000420193 (9:41985557 T>A), RS1000440786 (9:42101719 G>T), RS1000490521 (9:42126332 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

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, decreases expression, increases abundance, increases expression	2
Valproic Acid	decreases expression, increases expression	2
aristolochic acid I	decreases expression	1
perfluorooctanoic acid	decreases expression	1
tobacco tar	decreases expression	1
manganese chloride	decreases expression, increases abundance, affects cotreatment	1
S-(1,2-dichlorovinyl)cysteine	decreases expression, affects response to substance, increases expression, affects cotreatment	1
perfluorooctane sulfonic acid	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
perfluorohexanesulfonic acid	decreases expression	1
abrine	decreases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	increases expression	1
dorsomorphin	increases expression, affects cotreatment	1
Acetaldehyde	increases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Lipopolysaccharides	affects response to substance, increases expression, affects cotreatment, decreases expression	1
Manganese	decreases expression, increases abundance, affects cotreatment	1
Phenylmercuric Acetate	affects cotreatment, increases expression	1
Silicon Dioxide	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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