CATSPER1

cation channel sperm associated 1, the group of Cation channels sperm associated

Basic information

Region (hg38): 11:66016752-66026479

Links

ENSG00000175294 ∙ NCBI:117144 ∙ OMIM:606389 ∙ HGNC:17116 ∙ Uniprot:Q8NEC5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• non-syndromic male infertility due to sperm motility disorder (Supportive), mode of inheritance: AR
• spermatogenic failure 7 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 7	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	19344877

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CATSPER1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CATSPER1 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			11	7	4	22
missense			77	14	3	94
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			3	1		4
non coding			9	1	9	19
Total	0	0	97	22	16

Variants in CATSPER1

This is a list of pathogenic ClinVar variants found in the CATSPER1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-66016764-ACT-A		Male infertility	Uncertain significance (Jun 14, 2016)
11-66016794-C-T		Spermatogenic failure 7	Uncertain significance (Jan 13, 2018)
11-66016827-C-T		Spermatogenic failure 7	Uncertain significance (Jan 13, 2018)
11-66016867-C-T		Spermatogenic failure 7	Uncertain significance (Jan 13, 2018)
11-66017075-C-T			Likely benign (Jan 01, 2023)
11-66017080-T-C		not specified	Uncertain significance (Oct 12, 2021)
11-66017086-C-T		not specified	Uncertain significance (Jan 09, 2024)
11-66017092-C-T		not specified	Likely benign (Aug 25, 2021)
11-66017107-G-A		Spermatogenic failure 7 • not specified	Uncertain significance (Aug 10, 2021)
11-66017131-C-T		not specified	Uncertain significance (Nov 17, 2022)
11-66017132-G-A		Spermatogenic failure 7	Uncertain significance (Jan 13, 2018)
11-66017182-T-G		Spermatogenic failure 7	Uncertain significance (Jan 12, 2018)
11-66017353-T-A			Benign (Jun 19, 2021)
11-66018845-A-C		not specified	Uncertain significance (Nov 08, 2022)
11-66018845-A-G		not specified	Uncertain significance (Nov 14, 2023)
11-66018863-C-T		not specified	Likely benign (Dec 16, 2023)
11-66018882-C-T		not specified	Uncertain significance (Jul 25, 2023)
11-66018915-A-G		Spermatogenic failure 7	Uncertain significance (Jan 13, 2018)
11-66020156-C-T		Spermatogenic failure 7	Uncertain significance (Jan 12, 2018)
11-66020157-G-A		Male infertility • not specified	Uncertain significance (Dec 17, 2023)
11-66020191-G-A		not specified	Uncertain significance (Sep 22, 2023)
11-66020194-C-A		not specified	Uncertain significance (Jun 23, 2021)
11-66020195-G-A		Spermatogenic failure 7	Benign (Nov 10, 2018)
11-66020296-C-T			Benign (Jun 19, 2021)
11-66020311-C-T		Spermatogenic failure 7	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CATSPER1	protein_coding	protein_coding	ENST00000312106	12	9766

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.01e-11	0.717	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.651	430	470	0.916	0.0000313	5196
Missense in Polyphen		86	94.638	0.90872		1210
Synonymous	0.409	186	193	0.963	0.0000132	1501
Loss of Function	1.60	22	31.7	0.693	0.00000148	356

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000271
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000478	0.0000462
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.00	0.00
South Asian	0.000163	0.000163
Other	0.000163	0.000163

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}.
• Disease: DISEASE: Spermatogenic failure 7 (SPGF7) [MIM:612997]: An infertility disorder characterized by non-motile sperm or sperm motility below the normal threshold, low sperm count, increased abnormally structured spermatozoa, and reduced semen volume. {ECO:0000269|PubMed:19344877}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Fertilization;Reproduction;Sperm Motility And Taxes (Consensus)

Intolerance Scores

• loftool: 0.114
• rvis_EVS: -0.48
• rvis_percentile_EVS: 22.82

Haploinsufficiency Scores

• pHI: 0.0218
• hipred: N
• hipred_score: 0.153
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.459

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Catsper1
• Phenotype: reproductive system phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;cell differentiation;flagellated sperm motility;regulation of ion transmembrane transport;sperm-egg recognition;regulation of cilium beat frequency involved in ciliary motility;calcium ion transmembrane transport
• Cellular component: plasma membrane;motile cilium;CatSper complex
• Molecular function: calcium activated cation channel activity;voltage-gated calcium channel activity;protein binding