KASH5
Basic information
Region (hg38): 19:49388219-49417990
Previous symbols: [ "CCDC155" ]
Links
Phenotypes
GenCC
Source:
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Spermatogenic failure 88; Premature ovarian failure 22 | 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; Obstetric | 29790874; 35587281; 35674372; 36864840 |
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KASH5 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 | |||||
| missense | 28 | 32 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 28 | 6 | 0 |
Variants in KASH5
This is a list of pathogenic ClinVar variants found in the KASH5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KASH5 | protein_coding | protein_coding | ENST00000447857 | 19 | 29777 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 2.34e-9 | 0.994 | 124596 | 0 | 62 | 124658 | 0.000249 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.17 | 253 | 311 | 0.813 | 0.0000179 | 3524 |
| Missense in Polyphen | 40 | 67.413 | 0.59335 | 943 | ||
| Synonymous | 2.03 | 95 | 124 | 0.768 | 0.00000656 | 1141 |
| Loss of Function | 2.54 | 20 | 36.6 | 0.546 | 0.00000175 | 408 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000717 | 0.000709 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000464 | 0.0000464 |
| European (Non-Finnish) | 0.000235 | 0.000230 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000393 | 0.000360 |
| Other | 0.000862 | 0.000826 |
dbNSFP
Source:
- Function
- FUNCTION: As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, involved in the connection between the nuclear lamina and the cytoskeleton. The nucleocytoplasmic interactions established by the LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in nuclear movement and positioning. Required for telomere attachment to nuclear envelope in the prophase of meiosis and for rapid telomere prophase movements implicating a SUN1/2:KASH5 LINC complex in which SUN1 and SUN2 seem to act at least partial redundantly. Required for homologue pairing during meiotic prophase in spermatocytes and probably oocytes. Essential for male and female gametogenesis. Recruits cytoplasmic dynein to telomere attachment sites at the nuclear envelope in spermatocytes. In oocytes is involved in meiotic resumption and spindle formation. {ECO:0000250|UniProtKB:Q80VJ8}.;
Recessive Scores
- pRec
- 0.0788
Intolerance Scores
- loftool
- 0.914
- rvis_EVS
- -0.18
- rvis_percentile_EVS
- 40.56
Haploinsufficiency Scores
- pHI
- hipred
- N
- hipred_score
- 0.179
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.242
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ccdc155
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype;
Gene ontology
- Biological process
- double-strand break repair via homologous recombination;actin filament organization;synapsis;spermatogenesis;telomere localization;oogenesis;spindle assembly;spindle localization;microtubule cytoskeleton organization involved in homologous chromosome segregation;chromosome localization to nuclear envelope involved in homologous chromosome segregation
- Cellular component
- chromosome, telomeric region;lateral element;nuclear outer membrane;integral component of membrane;meiotic nuclear membrane microtubule tethering complex;meiotic spindle pole
- Molecular function
- protein binding;identical protein binding;dynein complex binding