CNTNAP3

contactin associated protein family member 3, the group of Contactin associated protein family

Basic information

Region (hg38): 9:39064710-39288315

Links

ENSG00000106714 ∙ NCBI:79937 ∙ OMIM:610517 ∙ HGNC:13834 ∙ Uniprot:Q9BZ76 ∙ 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 CNTNAP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNTNAP3 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	1	4
missense			105	9		114
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	105	12	1

Variants in CNTNAP3

This is a list of pathogenic ClinVar variants found in the CNTNAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-39073925-T-C		not specified	Uncertain significance (Sep 15, 2021)
9-39073933-C-G		not specified	Uncertain significance (Feb 16, 2023)
9-39073958-G-T		not specified	Uncertain significance (Oct 22, 2021)
9-39078695-C-A		not specified	Uncertain significance (Jan 24, 2025)
9-39078705-G-C		not specified	Uncertain significance (Oct 06, 2023)
9-39078728-G-A		not specified	Uncertain significance (Apr 07, 2023)
9-39078737-G-C		not specified	Uncertain significance (Jan 23, 2024)
9-39078750-C-T		not specified	Uncertain significance (May 14, 2024)
9-39078764-A-C		not specified	Uncertain significance (Jan 22, 2024)
9-39078765-T-G		not specified	Uncertain significance (Jan 21, 2025)
9-39078770-G-A		not specified	Uncertain significance (Mar 21, 2023)
9-39078774-C-A		not specified	Uncertain significance (Jun 18, 2021)
9-39078834-C-G		not specified	Uncertain significance (Apr 25, 2023)
9-39078846-A-G		not specified	Uncertain significance (Nov 30, 2022)
9-39078887-G-A		not specified	Uncertain significance (May 08, 2024)
9-39078915-C-G		not specified	Uncertain significance (Dec 22, 2023)
9-39085754-T-C		not specified	Uncertain significance (Apr 22, 2022)
9-39085771-T-C		not specified	Uncertain significance (Nov 15, 2024)
9-39085813-C-T		not specified	Likely benign (Oct 30, 2023)
9-39086768-C-G		not specified	Uncertain significance (Apr 06, 2022)
9-39086775-C-A		not specified	Uncertain significance (Jan 29, 2024)
9-39086780-T-C		not specified	Uncertain significance (Oct 01, 2024)
9-39086816-T-G		not specified	Uncertain significance (Mar 28, 2024)
9-39086849-C-A		not specified	Uncertain significance (Oct 12, 2021)
9-39088451-T-A		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNTNAP3	protein_coding	protein_coding	ENST00000297668	24	215549

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.71e-11	0.998	125489	1	113	125603	0.000454

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.146	518	527	0.982	0.0000302	8224
Missense in Polyphen		128	150.66	0.84957		2910
Synonymous	-1.57	243	214	1.14	0.0000137	2569
Loss of Function	2.82	25	45.5	0.549	0.00000249	705

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00107	0.00106
Ashkenazi Jewish	0.00	0.00
East Asian	0.000871	0.000816
Finnish	0.00143	0.00143
European (Non-Finnish)	0.000200	0.000185
Middle Eastern	0.000871	0.000816
South Asian	0.000295	0.000294
Other	0.000998	0.000979

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0943

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.405
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.536

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cntnap3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: cell adhesion;cell recognition
• Cellular component: extracellular region;plasma membrane;integral component of membrane