GeneBe

CATSPER1

protein-coding

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

Gene summary

Calcium ions play a primary role in the regulation of sperm motility. This gene belongs to a family of putative cation channels that are specific to spermatozoa and localize to the flagellum. The protein family features a single repeat with six membrane-spanning segments and a predicted calcium-selective pore region. [provided by RefSeq, Jul 2008]

MANE transcript

NM_053054.4

Inheritance

AR

ClinVar variants

P:3U:153B:38

Top phenotype

Spermatogenic failure 7

gnomAD constraint

pLI —, LoF o/e 0.69

Max pathogenic AF

—

Genomic locus

chr11:66,016,752-66,026,479

External References & Databases

Ensembl (ENSG00000175294)NCBI Gene (117144)OMIM (606389)HGNC:17116GenCCUniProt (Q8NEC5)AlphaFoldClinVar (CATSPER1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~9.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

non-syndromic male infertility due to sperm motility disorderSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0017173

Submitter: Orphanet

spermatogenic failure 7LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0013070

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Spermatogenic failure 7AR

Manifestation: Genitourinary

Intervention: General

Rationale: 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

Refs: 19344877Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CATSPER1 variants in ClinVar

4 Conditions Cataloged
not specifiedTotal: 138
Spermatogenic failure 7Total: 60
not providedTotal: 22
CATSPER1-related disorderTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_053054.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
15
clinvar
11
clinvar
1
clinvar
 27
missense
136
clinvar
25
clinvar
1
clinvar
 162
nonsense
1
clinvar
 1
start loss
0
frameshift
2
clinvar
1
clinvar
 3
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total21153362194

Highest pathogenic variant AF is 0.000021737942

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_053054.4RefSeqNP_444282.312MANE Select
ENST00000312106.6EnsemblENSP00000309052.512MANE Select
XM_047426337.1RefSeqXP_047282293.110Standard
XM_047426338.1RefSeqXP_047282294.16Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Fertilization
  • Reproduction
  • Sperm Motility And Taxes

Biological Process

  • multicellular organism development
  • spermatogenesis
  • cell differentiation
  • flagellated sperm motility
  • regulation of ion transmembrane transport

Molecular Function

  • calcium activated cation channel activity
  • voltage-gated calcium channel activity
  • protein binding

Cellular Component

  • plasma membrane
  • motile cilium
  • CatSper complex

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000312106
Coding exons
12
Length
9766
Individuals with no LoFs
125714
Homozygous LoFs
0
Heterozygous LoFs
34
Defined
125748
p
0.000135
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.6514304700.9160.00003135196
Missense (PolyPhen)8694.6380.908721210
Synonymous0.4091861930.9630.00001321501
Loss of Function1.602231.70.6930.00000148356

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000190.00018rare
Latino/Admixed American0.0000870.000087rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.0000480.000046rare
European (Non-Finnish)0.000190.00018rare
South Asian0.000160.00016rare
Other0.000160.00016rare

dbNSFP Gene Annotations

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.;

Intolerance Scores

LoFtool
0.114
RVIS EVS
-0.48
RVIS percentile EVS
22.82

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
S
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.459

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
Feedback | API | MCP | Annotate VCF | Sitemap | About | Privacy & Terms
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.