SKA1

spindle and kinetochore associated complex subunit 1

Basic information

Region (hg38): 18:50375040-50394168

Previous symbols: [ "C18orf24" ]

Links

ENSG00000154839

∙ NCBI:220134 ∙ OMIM:616673 ∙ HGNC:28109 ∙ Uniprot:Q96BD8 ∙ 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 SKA1 gene.

not_specified (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SKA1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000145060.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			18 clinvar	2 clinvar		20
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	18	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SKA1	protein_coding	protein_coding	ENST00000285116	6	19179

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000170	0.690	125655	0	56	125711	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	95	127	0.747	0.00000643	1672
Missense in Polyphen		20	34.916	0.5728		503
Synonymous	0.219	42	43.8	0.958	0.00000217	452
Loss of Function	0.999	9	12.9	0.700	7.31e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000190	0.000185
Ashkenazi Jewish	0.000800	0.000794
East Asian	0.000164	0.000163
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000331	0.000325
Middle Eastern	0.000164	0.000163
South Asian	0.00	0.00
Other	0.000682	0.000652

dbNSFP

Source: dbNSFP

Function: FUNCTION: Component of the SKA1 complex, a microtubule-binding subcomplex of the outer kinetochore that is essential for proper chromosome segregation (PubMed:17093495, PubMed:19289083, PubMed:23085020). Required for timely anaphase onset during mitosis, when chromosomes undergo bipolar attachment on spindle microtubules leading to silencing of the spindle checkpoint (PubMed:17093495). The SKA1 complex is a direct component of the kinetochore-microtubule interface and directly associates with microtubules as oligomeric assemblies (PubMed:19289083). The complex facilitates the processive movement of microspheres along a microtubule in a depolymerization-coupled manner (PubMed:19289083). Affinity for microtubules is synergistically enhanced in the presence of the ndc-80 complex and may allow the ndc-80 complex to track depolymerizing microtubules (PubMed:23085020). In the complex, it mediates the interaction with microtubules (PubMed:19289083, PubMed:23085020). {ECO:0000269|PubMed:17093495, ECO:0000269|PubMed:19289083, ECO:0000269|PubMed:23085020}.;
Pathway: Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic (Consensus)

Recessive Scores

pRec: 0.0780

Intolerance Scores

loftool: 0.909
rvis_EVS: 0.26
rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

pHI: 0.0796
hipred: Y
hipred_score: 0.531
ghis: 0.539

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ska1
Phenotype

Gene ontology

Biological process: mitotic cell cycle;chromosome segregation;regulation of microtubule polymerization or depolymerization;cell division
Cellular component: condensed chromosome outer kinetochore;cytosol;spindle microtubule;microtubule cytoskeleton
Molecular function: protein binding;microtubule binding