CNTNAP5

contactin associated protein family member 5, the group of Contactin associated protein family

Basic information

Region (hg38): 2:124025286-124921219

Links

ENSG00000155052 ∙ NCBI:129684 ∙ OMIM:610519 ∙ HGNC:18748 ∙ Uniprot:Q8WYK1 ∙ 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 CNTNAP5 gene.

• Inborn genetic diseases (50 variants)
• not provided (29 variants)
• CNTNAP5-related condition (4 variants)
• CNTNAP5-associated intellectual disability (1 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNTNAP5 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			1	9	1	11
missense			56	4	3	63
nonsense			2			2
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)			2			2
splice region				1	2	3
non coding					1	1
Total	0	0	63	13	5

Variants in CNTNAP5

This is a list of pathogenic ClinVar variants found in the CNTNAP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-124025707-G-T		not specified	Uncertain significance (Sep 27, 2021)
2-124025730-A-C			Benign (Sep 25, 2018)
2-124221810-G-A		CNTNAP5-related disorder	Uncertain significance (Aug 06, 2023)
2-124242203-C-T		not specified	Uncertain significance (May 18, 2023)
2-124242240-G-C		not specified	Uncertain significance (Jan 16, 2024)
2-124242291-G-A		CNTNAP5-related disorder	Likely benign (Jun 21, 2019)
2-124242303-C-T		CNTNAP5-related disorder	Likely benign (Mar 29, 2019)
2-124242304-G-A			Uncertain significance (Nov 10, 2023)
2-124242357-C-T		CNTNAP5-related disorder	Likely benign (Apr 01, 2024)
2-124417472-C-T		CNTNAP5-related disorder	Benign (Oct 28, 2019)
2-124417473-G-A		not specified	Uncertain significance (Jan 04, 2024)
2-124417519-G-A		not specified	Uncertain significance (Jun 07, 2023)
2-124434511-G-A		not specified	Uncertain significance (Jan 10, 2023)
2-124434541-A-G		not specified	Uncertain significance (Jan 03, 2024)
2-124434547-T-A		not specified	Uncertain significance (Feb 27, 2024)
2-124434572-C-T		CNTNAP5-related disorder	Likely benign (Sep 13, 2019)
2-124434590-G-A		not specified	Uncertain significance (Feb 23, 2023)
2-124434669-G-A		not specified	Uncertain significance (Jun 22, 2021)
2-124434676-A-G		not specified	Uncertain significance (Jul 19, 2023)
2-124434689-T-C		not specified	Uncertain significance (Oct 02, 2020)
2-124446767-C-T		not specified	Uncertain significance (Aug 28, 2023)
2-124446771-T-C		CNTNAP5-related disorder	Likely benign (Mar 01, 2023)
2-124446912-C-T		not specified	Uncertain significance (Feb 16, 2023)
2-124446928-T-G		not specified	Uncertain significance (Sep 27, 2021)
2-124474758-C-G			Uncertain significance (Apr 14, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNTNAP5	protein_coding	protein_coding	ENST00000431078	24	890001

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.992	0.00833	124751	0	26	124777	0.000104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.388	700	729	0.960	0.0000407	8551
Missense in Polyphen		176	247.43	0.71131		3019
Synonymous	-1.16	324	299	1.09	0.0000185	2497
Loss of Function	6.24	12	67.2	0.178	0.00000375	745

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000269	0.000269
Ashkenazi Jewish	0.000104	0.0000993
East Asian	0.0000556	0.0000556
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000993	0.0000971
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000656	0.0000654
Other	0.000332	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the correct development and proper functioning of the peripheral and central nervous system and be involved in cell adhesion and intercellular communication.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.298
• rvis_EVS: -0.99
• rvis_percentile_EVS: 8.65

Haploinsufficiency Scores

• pHI: 0.290
• hipred: N
• hipred_score: 0.488
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.446

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cntnap5a

Gene ontology

• Biological process: cell adhesion
• Cellular component: integral component of membrane