SPATA9

spermatogenesis associated 9

Basic information

Region (hg38): 5:95652180-95698711

Links

ENSG00000145757 ∙ NCBI:83890 ∙ OMIM:608039 ∙ HGNC:22988 ∙ Uniprot:Q9BWV2 ∙ 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 SPATA9 gene.

• Inborn genetic diseases (19 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA9 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2			2
non coding			4			4
Total	0	0	17	1	0

Variants in SPATA9

This is a list of pathogenic ClinVar variants found in the SPATA9 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-95654152-A-G		not specified	Uncertain significance (Nov 30, 2022)
5-95654219-T-C		not specified	Uncertain significance (Jun 24, 2022)
5-95654227-C-A		not specified	Uncertain significance (Oct 26, 2021)
5-95654227-C-T		not specified	Uncertain significance (Jan 06, 2023)
5-95656076-C-T		not specified	Uncertain significance (Mar 21, 2022)
5-95656077-C-G		not specified	Uncertain significance (Sep 06, 2022)
5-95656092-A-G		not specified	Uncertain significance (Nov 14, 2023)
5-95656230-C-A		not specified	Uncertain significance (Nov 06, 2023)
5-95658638-C-G		not specified	Uncertain significance (May 23, 2023)
5-95658675-T-G		not specified	Uncertain significance (Sep 14, 2022)
5-95658723-A-G		not specified	Uncertain significance (Jun 05, 2023)
5-95658802-G-T		not specified	Uncertain significance (Jan 24, 2024)
5-95658803-C-T			Likely benign (Dec 01, 2022)
5-95658813-G-T		not specified	Uncertain significance (Mar 04, 2024)
5-95658855-G-T		not specified	Uncertain significance (Nov 17, 2022)
5-95658895-C-T		not specified	Uncertain significance (Sep 16, 2021)
5-95658906-C-G		not specified	Uncertain significance (Jun 14, 2023)
5-95658909-A-T		not specified	Uncertain significance (Feb 22, 2023)
5-95675414-G-T		not specified	Uncertain significance (Mar 02, 2023)
5-95675423-A-T		not specified	Uncertain significance (Oct 03, 2022)
5-95675437-G-A		not specified	Uncertain significance (Jan 30, 2024)
5-95675441-C-T		not specified	Uncertain significance (May 05, 2023)
5-95675453-T-C		not specified	Uncertain significance (Feb 23, 2023)
5-95675525-C-G		not specified	Uncertain significance (May 23, 2023)
5-95675577-A-T		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA9	protein_coding	protein_coding	ENST00000274432	5	46531

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000348	0.604	125673	0	75	125748	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.670	108	129	0.834	0.00000637	1650
Missense in Polyphen		18	29.895	0.6021		423
Synonymous	0.769	41	47.8	0.858	0.00000246	483
Loss of Function	0.771	8	10.7	0.746	5.14e-7	154

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00125	0.00125
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000144	0.000141
Middle Eastern	0.000163	0.000163
South Asian	0.000600	0.000555
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in testicular development/spermatogenesis and may be an important factor in male infertility. {ECO:0000269|PubMed:12493713}.

Intolerance Scores

• loftool: 0.757
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

• pHI: 0.0553
• hipred: N
• hipred_score: 0.169
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.181

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata9
• Phenotype: normal phenotype

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;biological_process;cell differentiation
• Cellular component: cellular_component;integral component of membrane
• Molecular function: molecular_function