SPAG9

sperm associated antigen 9

Basic information

Region (hg38): 17:50962173-51120868

Links

ENSG00000008294 ∙ NCBI:9043 ∙ OMIM:605430 ∙ HGNC:14524 ∙ Uniprot:O60271 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPAG9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPAG9 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	3
missense			67	2		69
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1	3	4
Total	0	0	68	3	6

Variants in SPAG9

This is a list of pathogenic ClinVar variants found in the SPAG9 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-50966350-A-T		not specified	Uncertain significance (Jun 13, 2024)
17-50966364-G-A		not specified	Uncertain significance (Nov 04, 2023)
17-50970712-C-T		not specified	Uncertain significance (Jun 04, 2024)
17-50970752-T-C		not specified	Uncertain significance (Jun 24, 2022)
17-50970782-C-T		not specified	Uncertain significance (Dec 07, 2023)
17-50970824-C-T		not specified	Uncertain significance (Feb 28, 2024)
17-50974800-T-A		not specified	Uncertain significance (Nov 21, 2022)
17-50974804-G-A		not specified	Uncertain significance (Aug 09, 2021)
17-50974812-T-C		not specified	Uncertain significance (Jan 06, 2023)
17-50974900-G-A		not specified	Uncertain significance (Dec 06, 2022)
17-50974932-C-T		not specified	Uncertain significance (Jul 09, 2021)
17-50977137-C-G		not specified	Uncertain significance (Sep 22, 2023)
17-50979869-C-T		not specified	Uncertain significance (Nov 13, 2023)
17-50982628-G-A		not specified	Uncertain significance (Oct 27, 2022)
17-50982647-A-G			Benign (Dec 31, 2019)
17-50984913-C-T			Benign (Dec 31, 2018)
17-50984926-C-A		not specified	Uncertain significance (Jan 26, 2023)
17-50984941-T-C		not specified	Uncertain significance (Feb 23, 2023)
17-50985714-A-C		not specified	Uncertain significance (Jun 03, 2022)
17-50987169-T-G		not specified	Uncertain significance (Nov 09, 2021)
17-50989671-T-C			Likely benign (May 18, 2018)
17-50989693-G-C		not specified	Uncertain significance (Mar 04, 2024)
17-50989700-G-T		not specified	Uncertain significance (Aug 08, 2022)
17-50989710-A-G		not specified	Uncertain significance (Aug 21, 2023)
17-50989713-T-C		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPAG9	protein_coding	protein_coding	ENST00000262013	30	158692

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	6.54e-9	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.13	479	715	0.670	0.0000370	8651
Missense in Polyphen		102	217.98	0.46793		2449
Synonymous	1.18	234	258	0.907	0.0000136	2507
Loss of Function	7.43	5	74.0	0.0676	0.00000393	896

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000444	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000658	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The JNK-interacting protein (JIP) group of scaffold proteins selectively mediates JNK signaling by aggregating specific components of the MAPK cascade to form a functional JNK signaling module. Isoform 5 may play a role in spermatozoa-egg- interaction. {ECO:0000269|PubMed:14743216, ECO:0000269|PubMed:15693750}.
• Pathway: EGF-Ncore;Developmental Biology;CDO in myogenesis;Myogenesis;Arf6 trafficking events;TNFalpha (Consensus)

Recessive Scores

• pRec: 0.200

Intolerance Scores

• loftool: 0.399
• rvis_EVS: -1.13
• rvis_percentile_EVS: 6.56

Haploinsufficiency Scores

• pHI: 0.259
• hipred: Y
• hipred_score: 0.825
• ghis: 0.636

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.979

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spag9
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); pigmentation phenotype; reproductive system phenotype

Gene ontology

• Biological process: activation of JUN kinase activity;vesicle-mediated transport;positive regulation of cell migration;retrograde transport, endosome to Golgi;positive regulation of neuron differentiation;striated muscle cell differentiation;positive regulation of muscle cell differentiation;protein homooligomerization
• Cellular component: acrosomal vesicle;cytoplasm;microtubule organizing center;cytosol;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: MAP-kinase scaffold activity;protein binding;JUN kinase binding;kinesin binding;receptor signaling complex scaffold activity