CNTNAP3C

Summary

CNTNAP3C (contactin associated protein family member 3C, HGNC:53878) is a protein-coding gene on chromosome 9q12.

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

Source: NCBI Gene 100289279 — RefSeq curated summary.

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53878
Approved symbol	CNTNAP3C
Name	contactin associated protein family member 3C
Location	9q12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000283378
Ensembl biotype	protein_coding
Entrez	100289279

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000636699

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000636699 — 9 exons

Exon	Start	End
ENSE00003792581	61452887	61453030
ENSE00003792924	61379875	61380068
ENSE00003794646	61330717	61331052
ENSE00003795935	61441463	61441647
ENSE00003796308	61447338	61447599
ENSE00003796422	61352014	61352124
ENSE00003797075	61425702	61425849
ENSE00003798122	61442873	61443016
ENSE00003798230	61440605	61440808

Expression profiles

Bgee: expression breadth broad, 93 present calls, max score 80.89.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.89	gold quality
sural nerve	UBERON:0015488	80.16	gold quality
bone marrow	UBERON:0002371	71.70	gold quality
blood	UBERON:0000178	69.73	gold quality
bone marrow cell	CL:0002092	66.25	gold quality
mucosa of stomach	UBERON:0001199	60.76	gold quality
lower esophagus muscularis layer	UBERON:0035833	57.63	gold quality
lower esophagus	UBERON:0013473	57.60	gold quality
cortical plate	UBERON:0005343	56.64	gold quality
corpus callosum	UBERON:0002336	55.02	gold quality
colonic epithelium	UBERON:0000397	53.09	silver quality
esophagus	UBERON:0001043	52.50	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	52.42	gold quality
right atrium auricular region	UBERON:0006631	51.85	gold quality
tonsil	UBERON:0002372	51.63	silver quality
esophagogastric junction muscularis propria	UBERON:0035841	51.59	gold quality
placenta	UBERON:0001987	51.52	gold quality
skin of abdomen	UBERON:0001416	50.32	gold quality
right lung	UBERON:0002167	48.77	gold quality
zone of skin	UBERON:0000014	48.32	gold quality
esophagus mucosa	UBERON:0002469	47.45	gold quality
islet of Langerhans	UBERON:0000006	46.80	gold quality
skin of leg	UBERON:0001511	46.78	gold quality
heart	UBERON:0000948	46.21	gold quality
ventricular zone	UBERON:0003053	45.82	gold quality
minor salivary gland	UBERON:0001830	44.78	gold quality
saliva-secreting gland	UBERON:0001044	44.37	gold quality
muscle tissue	UBERON:0002385	43.82	gold quality
right uterine tube	UBERON:0001302	43.79	silver quality
calcaneal tendon	UBERON:0003701	43.78	silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.06

Regulation

Is transcription factor: no

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), CNTNAP3B (ENSG00000154529), 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)

Protein

Protein identifiers

Canonical reviewed UniProt: None (reviewed: )

All UniProt accessions (1): A0A1B0GTE1

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 1 (showing top): chr9q12

GO Biological Process (0):

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 anatomical structure	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

3198 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:61379886:T:A	W70R	0.998
9:61379886:T:C	W70R	0.998
9:61379961:G:C	A95P	0.998
9:61379888:G:C	W70C	0.997
9:61379888:G:T	W70C	0.997
9:61379968:A:C	Q97P	0.994
9:61379959:T:A	V94D	0.993
9:61380038:G:C	W120C	0.993
9:61380038:G:T	W120C	0.993
9:61425778:G:C	R156P	0.993
9:61425823:G:C	R171P	0.993
9:61379920:T:C	L81P	0.992
9:61379969:A:C	Q97H	0.992
9:61379969:A:T	Q97H	0.992
9:61447462:G:C	R399P	0.992
9:61380036:T:A	W120R	0.991
9:61380036:T:C	W120R	0.991
9:61425716:C:A	N135K	0.991
9:61425716:C:G	N135K	0.991
9:61379970:G:A	G98R	0.990
9:61379970:G:C	G98R	0.990
9:61425781:T:C	F157S	0.990
9:61379955:G:C	A93P	0.989
9:61379971:G:A	G98E	0.989
9:61379971:G:T	G98V	0.989
9:61380003:T:G	Y109D	0.989
9:61425838:G:A	G176E	0.988
9:61452912:G:C	W453C	0.988
9:61452912:G:T	W453C	0.988
9:61379993:G:C	W105C	0.987

dbSNP variants (sampled 300 via entrez): RS1000104938 (9:61406631 C>G), RS1000140106 (9:61344373 C>A,T), RS1000184691 (9:61375628 G>A), RS1000342225 (9:61370671 TC>T,TCC), RS1000356365 (9:61416084 T>G), RS1000428464 (9:61344083 A>T), RS1000523773 (9:61400243 T>A), RS1000538226 (9:61337719 A>G), RS1000603107 (9:61338108 C>T), RS1000616571 (9:61378000 G>C), RS1000717249 (9:61377642 G>GC), RS1000721478 (9:61385941 CAAAG>C), RS1000816774 (9:61386392 G>A), RS1000860567 (9:61363357 C>T), RS1000961867 (9:61417755 G>A)

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

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aminomethylphosphonic acid (AMPA)	increases expression	1
ethyl-p-hydroxybenzoate	decreases expression	1
sodium arsenite	increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
2,4-Dichlorophenoxyacetic Acid	increases expression	1
S-Nitrosoglutathione	increases expression	1

Clinical trials (associated diseases)

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