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.

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.

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				3	1	4
missense			82	11		93
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	83	14	1

Variants in SPAG5

This is a list of pathogenic ClinVar variants found in the SPAG5 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-28577742-C-G		not specified	Uncertain significance (Feb 17, 2023)
17-28577755-G-C		not specified	Uncertain significance (Sep 12, 2023)
17-28578051-C-T		not specified	Uncertain significance (Jan 02, 2024)
17-28578238-T-C		not specified	Uncertain significance (Sep 20, 2023)
17-28578261-A-T		not specified	Uncertain significance (Apr 15, 2024)
17-28578274-T-C		not specified	Uncertain significance (Dec 10, 2024)
17-28578276-A-G		not specified	Uncertain significance (Sep 01, 2021)
17-28578277-C-A		not specified	Uncertain significance (Apr 06, 2024)
17-28578372-C-T			Uncertain significance (Feb 28, 2020)
17-28578387-A-G		not specified	Uncertain significance (Jul 23, 2024)
17-28578407-T-C		not specified	Likely benign (Oct 03, 2022)
17-28578417-T-C		not specified	Likely benign (Feb 23, 2023)
17-28578489-G-A		not specified	Uncertain significance (Nov 18, 2022)
17-28578498-G-A		not specified	Uncertain significance (Nov 12, 2024)
17-28578501-T-C		not specified	Uncertain significance (Jan 09, 2024)
17-28578694-A-G		not specified	Uncertain significance (Mar 07, 2024)
17-28578725-G-T		not specified	Uncertain significance (Feb 14, 2024)
17-28578727-A-G		not specified	Uncertain significance (Mar 31, 2023)
17-28578735-C-G		not specified	Uncertain significance (Dec 16, 2024)
17-28579155-A-G		not specified	Uncertain significance (Nov 17, 2022)
17-28579179-T-A		not specified	Uncertain significance (Nov 13, 2024)
17-28579248-C-T		not specified	Uncertain significance (May 08, 2024)
17-28579387-T-A		not specified	Uncertain significance (Jan 03, 2024)
17-28579419-C-A		not specified	Uncertain significance (Jan 21, 2025)
17-28579444-T-C		not specified	Uncertain significance (Jan 16, 2024)

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