CNTN5

protein-coding

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

Gene summary

The protein encoded by this gene is a member of the immunoglobulin superfamily, and contactin family, which mediate cell surface interactions during nervous system development. This protein is a glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein that functions as a cell adhesion molecule. It may play a role in the formation of axon connections in the developing nervous system. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]

MANE transcript

NM_014361.4

Inheritance

—

ClinVar variants

U:189B:27

Top phenotype

CNTN5-related disorder

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr11:99,020,949-100,358,885

External References & Databases

Ensembl (ENSG00000149972)

Transcript & Mutation Effects

hg38 • Region Span ~1,337.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CNTN5 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 167

CNTN5-related disorderTotal: 25

not providedTotal: 17

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

CNTN5-related Neurodevelopmental disorderTotal: 1

Hirschsprung disease, susceptibility to, 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014361.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			6 clinvar	8 clinvar	4 clinvar	18
missense			177 clinvar	9 clinvar	6 clinvar	192
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	189	17	10	216

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014361.4	RefSeq	NP_055176.1	23	MANE Select
ENST00000524871.6	Ensembl	ENSP00000435637.1	23	MANE Select
NM_001243270.2	RefSeq	NP_001230199.1	23	Standard
NM_001243271.2	RefSeq	NP_001230200.1	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational modification: synthesis of GPI-anchored proteins
Post-translational protein modification
Metabolism of proteins

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

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000524871
Coding exons: 23
Length: 1337934
Individuals with no LoFs: 124301
Homozygous LoFs: 0
Heterozygous LoFs: 357
Defined: 124658
p: 0.00143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.336	599	576	1.04	0.0000305	7024
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.023	0.019	notable
Latino/Admixed American	0.0011	0.0010	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00012	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00016	0.00015	rare
South Asian	0.00025	0.00023	rare
Other	0.00019	0.00017	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.210

Intolerance Scores

LoFtool: 0.888
RVIS EVS: -0.08
RVIS percentile EVS: 47.22

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.163

Gene Damage Prediction

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