CNTN6

contactin 6, the group of Contactins|I-set domain containing

Basic information

Region (hg38): 3:1092657-1404217

Links

ENSG00000134115 ∙ NCBI:27255 ∙ OMIM:607220 ∙ HGNC:2176 ∙ Uniprot:Q9UQ52 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (Limited), mode of inheritance: Unknown
• complex neurodevelopmental disorder (Disputed Evidence), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CNTN6 gene.

• Inborn genetic diseases (52 variants)
• not provided (22 variants)
• CNTN6-related condition (4 variants)
• not specified (3 variants)
• Autistic behavior (1 variants)
• Autism spectrum disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNTN6 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	7	9
missense			57	4	5	66
nonsense		1			1	2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1	1			2
splice region			1		2	3
non coding					1	1
Total	0	2	58	6	14

Highest pathogenic variant AF is 0.00000659

Variants in CNTN6

This is a list of pathogenic ClinVar variants found in the CNTN6 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-1148024-A-G		CNTN6-related disorder	Uncertain significance (Feb 01, 2023)
3-1148048-A-T		not specified	Uncertain significance (Jan 04, 2024)
3-1220695-C-A		not specified	Uncertain significance (Dec 01, 2022)
3-1220704-C-T		not specified	Uncertain significance (Apr 07, 2023)
3-1220720-A-T		not specified	Uncertain significance (Jan 17, 2024)
3-1220750-A-T		not specified	Uncertain significance (Apr 18, 2023)
3-1220761-T-C		not specified	Uncertain significance (Apr 17, 2023)
3-1220770-A-G		not specified	Uncertain significance (Jun 29, 2023)
3-1220802-G-A		CNTN6-related disorder	Likely benign (Dec 23, 2019)
3-1227923-C-T		CNTN6-related disorder	Benign (Dec 31, 2019)
3-1227930-C-A		not specified	Uncertain significance (Mar 01, 2024)
3-1227974-G-A			Benign (Aug 22, 2018)
3-1278437-C-T		CNTN6-related disorder	Likely benign (Jun 04, 2019)
3-1278457-C-T			Benign (Nov 01, 2023)
3-1278462-A-T		not specified	Uncertain significance (Sep 29, 2023)
3-1278503-T-C		CNTN6-related disorder	Benign (Jan 13, 2020)
3-1295612-G-A		not specified	Uncertain significance (Aug 02, 2022)
3-1295633-C-A		not specified	Uncertain significance (Nov 21, 2023)
3-1295634-C-G		not specified	Uncertain significance (Jan 26, 2022)
3-1295642-G-A		not specified	Uncertain significance (Mar 31, 2022)
3-1295687-T-C			Benign (Dec 01, 2023)
3-1295706-A-G		CNTN6-related disorder	Uncertain significance (Jun 29, 2023)
3-1295708-C-T		not specified	Uncertain significance (Sep 13, 2023)
3-1295712-C-A		Autistic behavior	Likely pathogenic (Jul 16, 2018)
3-1295725-C-A		not specified	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNTN6	protein_coding	protein_coding	ENST00000446702	22	311642

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.02e-31	0.000350	125279	1	467	125747	0.00186

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.00	735	539	1.36	0.0000265	6690
Missense in Polyphen		285	227.64	1.252		2851
Synonymous	-3.62	258	194	1.33	0.00000996	1973
Loss of Function	0.620	49	53.9	0.909	0.00000271	655

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00364	0.00364
Ashkenazi Jewish	0.0133	0.0133
East Asian	0.00192	0.00185
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00126	0.00123
Middle Eastern	0.00192	0.00185
South Asian	0.00145	0.00144
Other	0.000985	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Contactins mediate cell surface interactions during nervous system development. Participates in oligodendrocytes generation by acting as a ligand of NOTCH1. Its association with NOTCH1 promotes NOTCH1 activation through the released notch intracellular domain (NICD) and subsequent translocation to the nucleus. Involved in motor coordination (By similarity). {ECO:0000250}.
• Pathway: Pathways Affected in Adenoid Cystic Carcinoma;Canonical and Non-canonical Notch signaling;Developmental Biology;CHL1 interactions;L1CAM interactions;Notch signaling pathway;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.974
• rvis_EVS: -0.92
• rvis_percentile_EVS: 9.81

Haploinsufficiency Scores

• pHI: 0.447
• hipred: N
• hipred_score: 0.144
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.140

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cntn6
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;Notch signaling pathway;axon guidance;central nervous system development;positive regulation of Notch signaling pathway;dendrite self-avoidance
• Cellular component: plasma membrane;axon;parallel fiber to Purkinje cell synapse;anchored component of presynaptic membrane
• Molecular function: Notch binding;cell-cell adhesion mediator activity