CATSPER4

cation channel sperm associated 4, the group of Cation channels sperm associated

Basic information

Region (hg38): 1:26190561-26202968

Links

ENSG00000188782 ∙ NCBI:378807 ∙ OMIM:609121 ∙ HGNC:23220 ∙ Uniprot:Q7RTX7 ∙ 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 CATSPER4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CATSPER4 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			32	2		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	2	3

Variants in CATSPER4

This is a list of pathogenic ClinVar variants found in the CATSPER4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-26190682-G-A		not specified	Uncertain significance (Jul 20, 2022)
1-26190709-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-26190727-G-A		not specified	Uncertain significance (Jun 28, 2022)
1-26190748-C-T		not specified	Uncertain significance (Nov 07, 2022)
1-26190775-C-T		not specified	Uncertain significance (Apr 22, 2024)
1-26190784-T-G		not specified	Uncertain significance (Jan 23, 2023)
1-26190820-C-A		not specified	Uncertain significance (Jul 05, 2023)
1-26190830-C-T		not specified	Likely benign (May 29, 2024)
1-26191290-G-A		not specified	Likely benign (Mar 31, 2023)
1-26191290-G-T		not specified	Uncertain significance (Feb 27, 2024)
1-26191311-A-G		not specified	Uncertain significance (Mar 29, 2023)
1-26191317-C-T		not specified	Uncertain significance (Apr 18, 2023)
1-26191358-A-T		not specified	Uncertain significance (Jun 16, 2024)
1-26191425-G-A		not specified	Uncertain significance (Sep 17, 2021)
1-26193812-T-C		not specified	Uncertain significance (Dec 07, 2023)
1-26193863-T-C		not specified	Uncertain significance (Mar 16, 2022)
1-26193865-A-G		not specified	Uncertain significance (Nov 16, 2021)
1-26197696-A-G		not specified	Uncertain significance (Aug 17, 2022)
1-26197734-C-G		not specified	Likely benign (Aug 10, 2023)
1-26197743-A-T		not specified	Uncertain significance (Feb 06, 2024)
1-26197749-G-T			not provided (-)
1-26197755-A-G		not specified	Uncertain significance (Jan 11, 2023)
1-26197965-G-A		not specified	Uncertain significance (Apr 04, 2023)
1-26197982-A-C		not specified	Uncertain significance (Oct 18, 2021)
1-26198001-C-T		not specified	Uncertain significance (Mar 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CATSPER4	protein_coding	protein_coding	ENST00000456354	10	12408

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.71e-11	0.384	125666	0	82	125748	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.374	263	281	0.937	0.0000169	3123
Missense in Polyphen		66	90.928	0.72585		1128
Synonymous	0.114	109	111	0.986	0.00000683	899
Loss of Function	1.08	19	24.8	0.765	0.00000131	250

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000528	0.000528
Middle Eastern	0.000272	0.000272
South Asian	0.000261	0.000261
Other	0.000326	0.000326

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: 0.0834

Intolerance Scores

• loftool: 0.153
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.45

Haploinsufficiency Scores

• pHI: 0.0745
• hipred: N
• hipred_score: 0.203

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.245

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Catsper4
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: sodium ion transport;multicellular organism development;flagellated sperm motility;regulation of ion transmembrane transport;sperm-egg recognition;sperm capacitation;calcium ion transmembrane transport
• Cellular component: acrosomal vesicle;plasma membrane;CatSper complex;sperm principal piece
• Molecular function: calcium activated cation channel activity;voltage-gated calcium channel activity