KASH5

KASH domain containing 5, the group of KASH domain containing

Basic information

Region (hg38): 19:49388219-49417990

Previous symbols: [ "CCDC155" ]

Links

ENSG00000161609 ∙ NCBI:147872 ∙ OMIM:618125 ∙ HGNC:26520 ∙ Uniprot:Q8N6L0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the KASH5 gene.

• not_specified (82 variants)
• Spermatogenic_failure_88 (6 variants)
• not_provided (3 variants)
• Premature_ovarian_failure_22 (3 variants)
• KASH5-related_disorder (1 variants)
• Azoospermia (1 variants)
• Genetic_non-acquired_premature_ovarian_failure (1 variants)

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. These statistics are base on transcript: NM_000144688.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous		1		2		3
missense	2		78	7		87
nonsense						0
start loss						0
frameshift	2					2
splice donor/acceptor (+/-2bp)						0
Total	4	1	78	9	0

Highest pathogenic variant AF is 0.0013597922

GnomAD

Source: gnomAD

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: dbNSFP

• 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

• hipred: N
• hipred_score: 0.179

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