CNTNAP4

contactin associated protein family member 4, the group of Contactin associated protein family

Basic information

Region (hg38): 16:76277278-76560757

Links

ENSG00000152910 ∙ NCBI:85445 ∙ OMIM:610518 ∙ HGNC:18747 ∙ Uniprot:Q9C0A0 ∙ 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 CNTNAP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNTNAP4 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		3
missense			20	3		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	20	6	1

Variants in CNTNAP4

This is a list of pathogenic ClinVar variants found in the CNTNAP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-76316490-G-A		not specified	Uncertain significance (Aug 15, 2023)
16-76355425-A-G			Uncertain significance (Apr 01, 2023)
16-76355486-A-G		not specified	Uncertain significance (Apr 13, 2022)
16-76427530-T-G		not specified	Uncertain significance (Mar 28, 2024)
16-76427535-C-T		not specified	Likely benign (Mar 01, 2024)
16-76427578-G-A		CNTNAP4-related disorder	Uncertain significance (Oct 27, 2023)
16-76448802-A-G		not specified	Uncertain significance (Nov 16, 2021)
16-76449739-C-T		not specified	Uncertain significance (Mar 21, 2023)
16-76452539-A-G		not specified	Uncertain significance (Jun 17, 2024)
16-76452626-A-G		CNTNAP4-related disorder	Likely benign (Feb 23, 2022)
16-76452687-G-A		not specified	Likely benign (Oct 10, 2023)
16-76452712-G-A		not specified	Uncertain significance (Apr 28, 2022)
16-76461945-C-A			Benign (Feb 22, 2019)
16-76462083-G-T		CNTNAP4-related disorder	Uncertain significance (May 02, 2024)
16-76479469-G-C		not specified	Uncertain significance (May 13, 2024)
16-76479473-T-A		CNTNAP4-related disorder	Likely benign (Apr 06, 2022)
16-76479493-G-C		not specified	Uncertain significance (Apr 16, 2024)
16-76489698-C-T		not specified	Uncertain significance (Aug 02, 2023)
16-76489748-C-T		not specified	Uncertain significance (Jul 12, 2022)
16-76489804-G-A		not specified	Likely benign (Nov 21, 2023)
16-76489856-A-G		not specified	Uncertain significance (Dec 21, 2022)
16-76494912-G-A		not specified	Uncertain significance (Sep 12, 2023)
16-76521280-A-T		CNTNAP4-related disorder	Likely benign (Mar 01, 2021)
16-76522108-C-A		not specified	Uncertain significance (May 14, 2024)
16-76538148-G-A		CNTNAP4-related disorder	Likely benign (Aug 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNTNAP4	protein_coding	protein_coding	ENST00000478060	23	281960

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.76e-7	1.00	125702	1	45	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.24	732	643	1.14	0.0000328	8065
Missense in Polyphen		158	203.3	0.77719		2615
Synonymous	-3.57	310	240	1.29	0.0000130	2334
Loss of Function	4.62	22	60.9	0.361	0.00000300	768

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000442	0.000431
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.0000557	0.0000544
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000173	0.000167
Middle Eastern	0.0000557	0.0000544
South Asian	0.000395	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Presynaptic protein involved in both dopaminergic synaptic transmission and GABAergic system, thereby participating in the structural maturation of inhibitory interneuron synapses. Involved in the dopaminergic synaptic transmission by attenuating dopamine release through a presynaptic mechanism. Also participates in the GABAergic system (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0980

Intolerance Scores

• loftool: 0.332
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.37

Haploinsufficiency Scores

• pHI: 0.230
• hipred: N
• hipred_score: 0.457
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.384

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cntnap4
• 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: cell adhesion;regulation of synaptic transmission, dopaminergic;regulation of synaptic transmission, GABAergic;regulation of synapse organization;regulation of grooming behavior
• Cellular component: cell junction;dendrite;presynaptic membrane;GABA-ergic synapse;integral component of presynaptic membrane