SPAG5

sperm associated antigen 5

Basic information

Region (hg38): 17:28577565-28599025

Links

ENSG00000076382

∙ NCBI:10615 ∙ OMIM:615562 ∙ HGNC:13452 ∙ Uniprot:Q96R06 ∙ 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 SPAG5 gene.

not_specified (142 variants)
not_provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPAG5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006461.4. 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				3 clinvar	1 clinvar	4
missense			126 clinvar	18 clinvar		144
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	127	21	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPAG5	protein_coding	protein_coding	ENST00000321765	24	21710

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.40e-15	1.00	125357	6	385	125748	0.00156

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	533	616	0.866	0.0000327	7795
Missense in Polyphen		168	186.25	0.90203		2583
Synonymous	0.466	225	234	0.961	0.0000115	2341
Loss of Function	3.40	35	64.4	0.543	0.00000323	736

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000354	0.000354
Ashkenazi Jewish	0.000497	0.000496
East Asian	0.000326	0.000326
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000423	0.000422
Middle Eastern	0.000326	0.000326
South Asian	0.0106	0.0104
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Essential component of the mitotic spindle required for normal chromosome segregation and progression into anaphase (PubMed:11724960, PubMed:12356910, PubMed:27462074). Required for chromosome alignment, normal timing of sister chromatid segregation, and maintenance of spindle pole architecture (PubMed:17664331, PubMed:27462074). In complex with SKAP, promotes stable microtubule-kinetochore attachments. May contribute to the regulation of separase activity. May regulate AURKA localization to mitotic spindle, but not to centrosomes and CCNB1 localization to both mitotic spindle and centrosomes (PubMed:18361916, PubMed:21402792). Involved in centriole duplication. Required for CDK5RAP2, CEP152, WDR62 and CEP63 centrosomal localization and promotes the centrosomal localization of CDK2 (PubMed:26297806). In non-mitotic cells, upon stress induction, inhibits mammalian target of rapamycin complex 1 (mTORC1) association and recruits the mTORC1 component RPTOR to stress granules (SGs), thereby preventing mTORC1 hyperactivation-induced apoptosis (PubMed:23953116). May enhance GSK3B-mediated phosphorylation of other substrates, such as MAPT/TAU (PubMed:18055457). {ECO:0000269|PubMed:12356910, ECO:0000269|PubMed:17664331, ECO:0000269|PubMed:18055457, ECO:0000269|PubMed:18361916, ECO:0000269|PubMed:21402792, ECO:0000269|PubMed:23953116, ECO:0000269|PubMed:26297806, ECO:0000269|PubMed:27462074, ECO:0000305|PubMed:11724960}.;

Recessive Scores

pRec: 0.135

Intolerance Scores

loftool: 0.246
rvis_EVS: -0.39
rvis_percentile_EVS: 27.08

Haploinsufficiency Scores

pHI: 0.335
hipred: N
hipred_score: 0.273
ghis: 0.603

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: E
gene_indispensability_pred: N
gene_indispensability_score: 0.233

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Spag5
Phenotype: normal phenotype;

Gene ontology

Biological process: mitotic sister chromatid segregation;spindle organization;chromosome segregation;positive regulation of intracellular transport;cell division;regulation of attachment of spindle microtubules to kinetochore;protein localization to centrosome;regulation of metaphase plate congression;positive regulation of spindle assembly
Cellular component: kinetochore;condensed chromosome kinetochore;cytoplasm;midbody;centriolar satellite;microtubule plus-end;mitotic spindle;mitotic spindle pole
Molecular function: protein binding;microtubule binding