CATSPER2

cation channel sperm associated 2, the group of Cation channels sperm associated

Basic information

Region (hg38): 15:43628503-43668118

Links

ENSG00000166762 ∙ NCBI:117155 ∙ OMIM:607249 ∙ HGNC:18810 ∙ Uniprot:Q96P56 ∙ 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 CATSPER2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CATSPER2 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				2		2
missense			29	5	3	37
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region				1	2	3
non coding				1	11	12
Total	0	0	30	8	15

Variants in CATSPER2

This is a list of pathogenic ClinVar variants found in the CATSPER2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-43630388-T-C			Benign (Nov 10, 2018)
15-43631976-C-G			Benign (Nov 10, 2018)
15-43632151-C-T			Likely benign (Nov 10, 2018)
15-43632216-T-A		not specified	Uncertain significance (Mar 24, 2023)
15-43632219-T-A		not specified	Uncertain significance (Jan 31, 2024)
15-43632268-G-A			Uncertain significance (Sep 06, 2022)
15-43632308-C-T		not specified	Uncertain significance (Nov 21, 2024)
15-43632322-C-T		not specified	Uncertain significance (Mar 01, 2023)
15-43632324-G-A		not specified	Uncertain significance (Feb 13, 2023)
15-43632361-G-A		not specified	Uncertain significance (Feb 28, 2024)
15-43632392-C-T			Benign (Nov 11, 2018)
15-43632410-T-C			Benign (Nov 11, 2018)
15-43632484-G-A			Benign (Nov 10, 2018)
15-43632744-A-G		not specified	Uncertain significance (Jun 07, 2024)
15-43632771-A-T		not specified	Uncertain significance (Dec 03, 2024)
15-43632772-G-T			Likely benign (Aug 01, 2022)
15-43632798-C-T		not specified	Likely benign (Nov 15, 2021)
15-43632843-T-C		not specified	Uncertain significance (Jun 30, 2024)
15-43632894-A-T			Benign (Nov 10, 2018)
15-43632936-T-A		not specified • Rare genetic deafness	Benign (May 28, 2019)
15-43632937-T-G		not specified • Rare genetic deafness	Benign (May 28, 2019)
15-43632942-A-G		not specified	Benign (May 09, 2017)
15-43632949-T-G			Benign (Nov 10, 2018)
15-43635172-T-C			Benign (Nov 10, 2018)
15-43635363-T-G		not specified	Uncertain significance (Aug 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CATSPER2	protein_coding	protein_coding	ENST00000321596	12	39616

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.86e-17	0.0259	61886	13954	49898	125738	0.298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.750	321	285	1.12	0.0000171	3462
Missense in Polyphen		78	83.152	0.93804		1060
Synonymous	-0.940	118	106	1.12	0.00000592	1013
Loss of Function	0.576	27	30.4	0.887	0.00000168	332

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	1.02	0.930
Ashkenazi Jewish	0.382	0.366
East Asian	0.329	0.323
Finnish	0.181	0.174
European (Non-Finnish)	0.275	0.267
Middle Eastern	0.329	0.323
South Asian	0.362	0.352
Other	0.306	0.293

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Voltage-gated calcium channel that plays a central role in calcium-dependent physiological responses essential for successful fertilization, such as sperm hyperactivation, acrosome reaction and chemotaxis towards the oocyte. {ECO:0000269|PubMed:21412338, ECO:0000269|PubMed:21412339}.
• Pathway: Fertilization;Reproduction;Sperm Motility And Taxes (Consensus)

Recessive Scores

• pRec: 0.0651

Intolerance Scores

• loftool: 0.164
• rvis_EVS: 0.91
• rvis_percentile_EVS: 89.51

Haploinsufficiency Scores

• pHI: 0.0372
• hipred: N
• hipred_score: 0.243
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0359

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Catsper2
• Phenotype: reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: multicellular organism development;fertilization;flagellated sperm motility;regulation of ion transmembrane transport;sperm-egg recognition;sperm capacitation;calcium ion transmembrane transport
• Cellular component: plasma membrane;motile cilium;CatSper complex
• Molecular function: calcium activated cation channel activity;voltage-gated ion channel activity;calcium channel activity;protein binding