CATSPERD

cation channel sperm associated auxiliary subunit delta, the group of Cation channels sperm associated

Basic information

Region (hg38): 19:5720637-5778734

Previous symbols: [ "TMEM146" ]

Links

ENSG00000174898 ∙ NCBI:257062 ∙ OMIM:617490 ∙ HGNC:28598 ∙ Uniprot:Q86XM0 ∙ 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 CATSPERD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CATSPERD 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			74	7		81
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	74	9	0

Variants in CATSPERD

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

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

Position	Type	Phenotype	Significance	ClinVar
19-5720748-T-C		not specified	Uncertain significance (Jun 19, 2024)
19-5720772-T-C		not specified	Uncertain significance (May 07, 2024)
19-5724849-A-G		not specified	Uncertain significance (Dec 13, 2023)
19-5724852-A-G		not specified	Uncertain significance (Mar 20, 2024)
19-5727283-C-T		not specified	Uncertain significance (Feb 27, 2024)
19-5727322-A-G		not specified	Uncertain significance (Feb 13, 2024)
19-5729879-G-A		not specified	Uncertain significance (Sep 08, 2024)
19-5729918-C-T		not specified	Uncertain significance (Aug 25, 2021)
19-5733881-C-T		not specified	Uncertain significance (Dec 05, 2022)
19-5733883-C-T		not specified	Uncertain significance (Feb 08, 2025)
19-5733892-G-T		not specified	Uncertain significance (Jan 03, 2024)
19-5733920-A-C		not specified	Uncertain significance (Jul 14, 2021)
19-5733963-G-A		not specified	Uncertain significance (Jul 19, 2023)
19-5737138-G-A		not specified	Uncertain significance (Nov 25, 2024)
19-5737189-G-C		not specified	Uncertain significance (Dec 04, 2024)
19-5739326-C-T		not specified	Uncertain significance (Jan 24, 2025)
19-5739356-C-T		not specified	Uncertain significance (Jun 09, 2022)
19-5739357-G-A		not specified	Likely benign (Jun 10, 2022)
19-5739429-A-G		not specified	Uncertain significance (Jul 16, 2024)
19-5744451-G-A		not specified	Uncertain significance (May 17, 2023)
19-5744490-C-G		not specified	Uncertain significance (Oct 13, 2023)
19-5744494-T-C		not specified	Uncertain significance (Dec 30, 2023)
19-5745947-G-A		not specified	Uncertain significance (Feb 19, 2025)
19-5746003-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-5748176-C-T		not specified	Likely benign (Nov 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CATSPERD	protein_coding	protein_coding	ENST00000381624	22	58058

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.51e-15	0.827	124673	0	132	124805	0.000529

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.227	452	466	0.970	0.0000266	5216
Missense in Polyphen		139	156.41	0.88867		1868
Synonymous	-1.23	218	196	1.11	0.0000130	1517
Loss of Function	1.97	29	43.0	0.675	0.00000192	511

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00119	0.00119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00123	0.00122
Finnish	0.00	0.00
European (Non-Finnish)	0.000577	0.000574
Middle Eastern	0.00123	0.00122
South Asian	0.000365	0.000360
Other	0.000499	0.000495

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Auxiliary component of the CatSper complex, a complex involved in sperm cell hyperactivation. Sperm cell hyperactivation is needed for sperm motility which is essential late in the preparation of sperm for fertilization. Required for CATSPER1 stability before intraflagellar transport and/or incorporation of the CatSper complex channel into the flagellar membrane. {ECO:0000250|UniProtKB:E9Q9F6}.
• Pathway: Fertilization;Reproduction;Sperm Motility And Taxes (Consensus)

Intolerance Scores

• rvis_EVS: 1.9
• rvis_percentile_EVS: 97.35

Haploinsufficiency Scores

• pHI: 0.0697
• hipred: N
• hipred_score: 0.233

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Catsperd
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;flagellated sperm motility;sperm-egg recognition;sperm capacitation
• Cellular component: plasma membrane;CatSper complex;sperm principal piece
• Molecular function: protein binding