SPATA3

spermatogenesis associated 3

Basic information

Region (hg38): 2:230990324-231025055

Links

ENSG00000173699 ∙ NCBI:130560 ∙ OMIM:619857 ∙ HGNC:17884 ∙ Uniprot:Q8NHX4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPATA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA3 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			15	3		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	4	0

Variants in SPATA3

This is a list of pathogenic ClinVar variants found in the SPATA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-230996396-C-T		not specified	Uncertain significance (Mar 26, 2024)
2-230996421-C-T		not specified	Uncertain significance (Jan 06, 2023)
2-230996426-C-T		not specified	Uncertain significance (Feb 22, 2023)
2-230996427-G-A		not specified	Likely benign (Dec 05, 2022)
2-230996469-G-C		not specified	Uncertain significance (Sep 01, 2021)
2-230996495-G-A			Likely benign (Mar 01, 2023)
2-230996505-T-G		not specified	Uncertain significance (Dec 07, 2023)
2-230996520-A-G		not specified	Likely benign (Jun 29, 2023)
2-231000380-G-A		not specified	Uncertain significance (Feb 17, 2022)
2-231000383-G-A		not specified	Uncertain significance (Jul 20, 2022)
2-231000413-C-T		not specified	Uncertain significance (Jun 06, 2023)
2-231000425-G-A		not specified	Uncertain significance (Sep 20, 2023)
2-231000439-T-C			Likely benign (Nov 01, 2022)
2-231000444-G-A		not specified	Uncertain significance (May 09, 2023)
2-231000450-G-T		not specified	Uncertain significance (Nov 03, 2022)
2-231000459-G-A		not specified	Uncertain significance (May 30, 2024)
2-231000482-C-T		not specified	Uncertain significance (Oct 10, 2023)
2-231000498-C-T		not specified	Uncertain significance (Sep 14, 2022)
2-231000500-C-A		not specified	Uncertain significance (Jul 19, 2023)
2-231002713-G-A		not specified	Uncertain significance (Jun 10, 2024)
2-231002719-C-T		not specified	Uncertain significance (May 09, 2023)
2-231002760-G-C		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA3	protein_coding	protein_coding	ENST00000452881	3	28935

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00107	0.623	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00490	102	102	1.00	0.00000613	1216
Missense in Polyphen		3	3.3498	0.89559		52
Synonymous	0.878	30	36.8	0.816	0.00000194	406
Loss of Function	0.570	5	6.58	0.760	3.66e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.79
• rvis_percentile_EVS: 87.4

Haploinsufficiency Scores

• pHI: 0.0262

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0557

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata3

Gene ontology

• Cellular component: cellular_component
• Molecular function: molecular_function