SKA3

spindle and kinetochore associated complex subunit 3

Basic information

Region (hg38): 13:21153595-21176552

Previous symbols: [ "C13orf3" ]

Links

ENSG00000165480 ∙ NCBI:221150 ∙ OMIM:619247 ∙ HGNC:20262 ∙ Uniprot:Q8IX90 ∙ 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 SKA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SKA3 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				1		1
missense			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in SKA3

This is a list of pathogenic ClinVar variants found in the SKA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-21155754-G-A		not specified	Uncertain significance (Jan 22, 2025)
13-21155757-G-T		not specified	Uncertain significance (Apr 20, 2023)
13-21157977-A-C		not specified	Uncertain significance (Aug 28, 2024)
13-21157999-T-A		not specified	Uncertain significance (Jul 25, 2023)
13-21158013-T-G		not specified	Uncertain significance (Jan 24, 2025)
13-21158020-A-C		not specified	Uncertain significance (Dec 23, 2024)
13-21158055-G-A		not specified	Uncertain significance (Nov 09, 2023)
13-21158113-A-G		not specified	Uncertain significance (Aug 04, 2024)
13-21158125-C-T		not specified	Uncertain significance (Jan 09, 2024)
13-21159906-G-A		not specified	Uncertain significance (May 30, 2024)
13-21159954-G-T		not specified	Uncertain significance (Dec 11, 2023)
13-21168003-G-A		not specified	Likely benign (Dec 28, 2024)
13-21168008-T-G		not specified	Uncertain significance (Feb 22, 2025)
13-21168058-T-C		not specified	Uncertain significance (Oct 09, 2024)
13-21168074-T-C			Likely benign (Mar 01, 2023)
13-21168101-C-T		not specified	Uncertain significance (Jul 09, 2024)
13-21168186-T-C		not specified	Uncertain significance (Jun 29, 2022)
13-21168217-G-C		not specified	Uncertain significance (Dec 12, 2023)
13-21168270-C-T		not specified	Uncertain significance (Dec 27, 2023)
13-21168271-G-A		not specified	Uncertain significance (Jan 15, 2025)
13-21168347-A-C		not specified	Uncertain significance (May 04, 2023)
13-21168366-T-C		not specified	Uncertain significance (Dec 28, 2022)
13-21172365-T-C		not specified	Uncertain significance (Dec 14, 2023)
13-21172399-T-C		not specified	Uncertain significance (Jul 29, 2023)
13-21172459-C-G		not specified	Uncertain significance (Jul 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SKA3	protein_coding	protein_coding	ENST00000314759	8	23008

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.51e-7	0.631	113135	0	12613	125748	0.0515

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.306	214	202	1.06	0.00000972	2665
Missense in Polyphen		38	55.244	0.68786		791
Synonymous	-0.522	79	73.3	1.08	0.00000362	766
Loss of Function	1.11	13	18.1	0.718	8.41e-7	261

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0682	0.0679
Ashkenazi Jewish	0.0464	0.0460
East Asian	0.0684	0.0677
Finnish	0.0634	0.0626
European (Non-Finnish)	0.0463	0.0453
Middle Eastern	0.0684	0.0677
South Asian	0.0774	0.0775
Other	0.0452	0.0443

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:19289083, PubMed:19360002, PubMed:23085020). The SKA1 complex is a direct component of the kinetochore-microtubule interface and directly associates with microtubules as oligomeric assemblies (PubMed:19289083, PubMed:19360002). The complex facilitates the processive movement of microspheres along a microtubule in a depolymerization-coupled manner (PubMed:19289083). In the complex, it mediates the microtubule-stimulated oligomerization (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). {ECO:0000269|PubMed:19289083, ECO:0000269|PubMed:19360002, ECO:0000269|PubMed:23085020}.

Recessive Scores

• pRec: 0.0782

Intolerance Scores

• loftool: 0.823
• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.3

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.396
• ghis: 0.537

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ska3

Gene ontology

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