CNTN5

contactin 5, the group of I-set domain containing|Contactins

Basic information

Region (hg38): 11:99020948-100358885

Links

ENSG00000149972 ∙ NCBI:53942 ∙ OMIM:607219 ∙ HGNC:2175 ∙ Uniprot:O94779 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CNTN5 gene.

• Inborn genetic diseases (50 variants)
• not provided (18 variants)
• CNTN5-related condition (3 variants)
• CNTN5-related Neurodevelopmental disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNTN5 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				3	4	7
missense			54	3	5	62
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	55	6	9

Variants in CNTN5

This is a list of pathogenic ClinVar variants found in the CNTN5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-99556237-T-A		Inborn genetic diseases	Uncertain significance (Jan 03, 2022)
11-99819682-C-A		not specified	Uncertain significance (Apr 11, 2023)
11-99819693-T-G		not specified	Uncertain significance (Aug 08, 2022)
11-99819695-G-T		not specified	Uncertain significance (Nov 22, 2021)
11-99819697-T-G			Benign (Jul 14, 2017)
11-99819703-C-A		not specified	Uncertain significance (Oct 22, 2021)
11-99819775-A-G		CNTN5-related disorder	Benign (May 21, 2020)
11-99844903-T-C		CNTN5-related disorder	Likely benign (Jun 06, 2019)
11-99844933-C-A		not specified	Uncertain significance (Jul 12, 2022)
11-99844951-G-A		not specified	Uncertain significance (Jun 06, 2023)
11-99844959-C-T		not specified	Uncertain significance (Aug 26, 2022)
11-99845149-G-A		not specified	Uncertain significance (Jan 23, 2023)
11-99845159-T-G		CNTN5-related disorder	Benign (Dec 31, 2019)
11-99845160-A-G		not specified	Uncertain significance (Oct 03, 2023)
11-99845165-C-T		CNTN5-related disorder	Likely benign (Mar 22, 2019)
11-99845236-G-A		not specified	Uncertain significance (Feb 06, 2024)
11-99916106-C-T			Likely benign (May 19, 2018)
11-99916135-C-A		not specified	Uncertain significance (Jan 16, 2024)
11-99956846-T-G		CNTN5-related Neurodevelopmental disorder	Uncertain significance (Mar 05, 2021)
11-99956933-T-C			Likely benign (Apr 01, 2022)
11-99956961-A-G		not specified	Uncertain significance (Jan 26, 2023)
11-100002039-A-T		not specified	Uncertain significance (Dec 06, 2021)
11-100002071-T-G		not specified	Uncertain significance (Feb 23, 2023)
11-100061207-C-T			Likely benign (Dec 01, 2022)
11-100061213-C-G		CNTN5-related disorder	Likely benign (Aug 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNTN5	protein_coding	protein_coding	ENST00000524871	23	1337934

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000620	1.00	124301	0	357	124658	0.00143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.336	599	576	1.04	0.0000305	7024
Missense in Polyphen		267	269.55	0.99053		3188
Synonymous	-1.77	241	209	1.16	0.0000114	2178
Loss of Function	4.62	18	55.0	0.327	0.00000284	688

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0240	0.0204
Ashkenazi Jewish	0.00	0.00
East Asian	0.000119	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000158	0.000150
Middle Eastern	0.000119	0.000111
South Asian	0.000252	0.000229
Other	0.000194	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Contactins mediate cell surface interactions during nervous system development. Has some neurite outgrowth-promoting activity in the cerebral cortical neurons but not in hippocampal neurons. Probably involved in neuronal activity in the auditory system (By similarity). {ECO:0000250}.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.210

Intolerance Scores

• loftool: 0.888
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.22

Haploinsufficiency Scores

• pHI: 0.294
• hipred: Y
• hipred_score: 0.544
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.163

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cntn5
• Phenotype: 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: cell adhesion;sensory perception of sound;presynapse assembly
• Cellular component: extracellular region;cytosol;plasma membrane;GABA-ergic synapse;anchored component of presynaptic membrane