CATSPER3

cation channel sperm associated 3, the group of Cation channels sperm associated

Basic information

Region (hg38): 5:134967907-135011696

Links

ENSG00000152705 ∙ NCBI:347732 ∙ OMIM:609120 ∙ HGNC:20819 ∙ Uniprot:Q86XQ3 ∙ 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 CATSPER3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CATSPER3 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	1
missense			23	2		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	1

Variants in CATSPER3

This is a list of pathogenic ClinVar variants found in the CATSPER3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-134968007-C-T		not specified	Uncertain significance (Sep 14, 2022)
5-134968020-C-T		not specified	Uncertain significance (Sep 14, 2023)
5-134968024-A-T		not specified	Uncertain significance (Aug 09, 2021)
5-134968032-C-G		not specified	Uncertain significance (Dec 08, 2023)
5-134968052-A-G		not specified	Likely benign (Nov 28, 2023)
5-134968056-C-T		not specified	Uncertain significance (Aug 08, 2023)
5-134968077-T-A		not specified	Uncertain significance (Apr 26, 2024)
5-134996330-G-A		not specified	Uncertain significance (Jul 14, 2022)
5-134996357-G-A		not specified	Uncertain significance (Dec 22, 2023)
5-134996384-A-G		not specified	Uncertain significance (Jul 30, 2023)
5-134996390-G-A		not specified	Likely benign (Jun 18, 2021)
5-134996423-A-C		not specified	Uncertain significance (Jul 14, 2021)
5-134996426-G-A		not specified	Uncertain significance (Aug 21, 2023)
5-134996426-G-T		not specified	Uncertain significance (Mar 07, 2023)
5-134996475-G-T		not specified	Uncertain significance (Feb 07, 2023)
5-135007987-T-C		not specified	Uncertain significance (Dec 03, 2021)
5-135008023-C-T		not specified	Uncertain significance (Aug 02, 2021)
5-135008063-G-A		not specified	Uncertain significance (Nov 14, 2023)
5-135008081-A-C		not specified	Uncertain significance (Mar 06, 2023)
5-135008100-C-A		not specified	Uncertain significance (Apr 16, 2024)
5-135008854-C-T		not specified	Uncertain significance (Nov 09, 2023)
5-135008880-C-T		not specified	Uncertain significance (Jul 12, 2022)
5-135008898-C-T		not specified	Uncertain significance (Apr 12, 2024)
5-135008955-G-A		not specified	Uncertain significance (Nov 28, 2023)
5-135009407-G-C		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CATSPER3	protein_coding	protein_coding	ENST00000282611	8	43797

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000752	0.925	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.328	235	221	1.06	0.0000134	2671
Missense in Polyphen		65	65.948	0.98563		846
Synonymous	0.859	74	84.0	0.881	0.00000513	726
Loss of Function	1.63	9	16.1	0.561	7.89e-7	193

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000329	0.000329
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000376	0.000370
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000109	0.000109
South Asian	0.000196	0.000196
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: 0.0864

Intolerance Scores

• loftool: 0.208
• rvis_EVS: 0.85
• rvis_percentile_EVS: 88.42

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.170
• ghis: 0.380

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0421

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Catsper3
• 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;endoplasmic reticulum;plasma membrane;motile cilium;CatSper complex
• Molecular function: voltage-gated calcium channel activity