SPATA9

spermatogenesis associated 9

Basic information

Region (hg38): 5:95652181-95698711

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.

• not_specified (28 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. These statistics are base on transcript: NM_000031952.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			28			28
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	28	1	0

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