SPATA2

spermatogenesis associated 2, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 20:49903391-49915529

Links

ENSG00000158480 ∙ NCBI:9825 ∙ OMIM:607662 ∙ HGNC:14681 ∙ Uniprot:Q9UM82 ∙ 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 SPATA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA2 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			44	1		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	2	0

Variants in SPATA2

This is a list of pathogenic ClinVar variants found in the SPATA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-49905630-C-T		not specified	Uncertain significance (Nov 18, 2022)
20-49905711-G-C		not specified	Uncertain significance (Jul 26, 2022)
20-49905788-C-T		not specified	Uncertain significance (Mar 14, 2023)
20-49905840-A-T		not specified	Uncertain significance (Sep 15, 2021)
20-49905858-G-A		not specified	Uncertain significance (Dec 16, 2023)
20-49905861-C-T		not specified	Uncertain significance (Jan 10, 2023)
20-49905872-G-T		not specified	Uncertain significance (Dec 22, 2023)
20-49905906-C-T		not specified	Uncertain significance (Nov 22, 2022)
20-49905912-C-T		not specified	Uncertain significance (Mar 26, 2024)
20-49905951-T-G		not specified	Uncertain significance (Jun 10, 2024)
20-49905993-G-A		not specified	Uncertain significance (Jul 15, 2021)
20-49906011-T-C		not specified	Uncertain significance (Mar 20, 2024)
20-49906013-C-T		not specified	Uncertain significance (May 15, 2024)
20-49906071-G-A		not specified	Uncertain significance (Nov 28, 2023)
20-49906088-T-C		not specified	Uncertain significance (Dec 19, 2022)
20-49906091-G-C		not specified	Uncertain significance (Nov 07, 2022)
20-49906185-C-G		not specified	Uncertain significance (Aug 23, 2021)
20-49906199-T-C		not specified	Uncertain significance (Jun 02, 2023)
20-49906206-C-T		not specified	Likely benign (Jun 16, 2023)
20-49906208-C-T		not specified	Uncertain significance (Nov 08, 2022)
20-49906256-G-C		not specified	Uncertain significance (May 24, 2023)
20-49906274-C-T		not specified	Uncertain significance (Oct 03, 2022)
20-49906279-C-A		not specified	Uncertain significance (Oct 03, 2022)
20-49906322-A-G		not specified	Uncertain significance (Sep 20, 2023)
20-49906329-C-T		not specified	Uncertain significance (Dec 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA2	protein_coding	protein_coding	ENST00000422556	2	12153

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.979	0.0211	125593	1	3	125597	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.677	305	340	0.897	0.0000230	3349
Missense in Polyphen		105	139.41	0.75315		1265
Synonymous	1.16	134	152	0.880	0.0000105	1091
Loss of Function	3.50	1	16.2	0.0617	9.35e-7	193

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000911	0.0000909
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000908	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000329	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Bridging factor that mediates the recruitment of CYLD to the LUBAC complex, thereby regulating TNF-alpha-induced necroptosis (PubMed:27307491, PubMed:27458237, PubMed:27545878, PubMed:27591049). Acts as a direct binding intermediate that bridges RNF31/HOIP, the catalytic subunit of the LUBAC complex, and the deubiquitinase (CYLD), thereby recruiting CYLD to the TNF- R1 signaling complex (TNF-RSC) (PubMed:27458237, PubMed:27545878, PubMed:27591049). Required to activate the 'Met-1'- (linear) and 'Lys-63'-linked deubiquitinase activities of CYLD (PubMed:27458237, PubMed:27591049). Controls the kinase activity of RIPK1 and TNF-alpha-induced necroptosis by promoting 'Met-1'- linked deubiquitination of RIPK1 by CYLD (By similarity). {ECO:0000250|UniProtKB:Q8K004, ECO:0000269|PubMed:27307491, ECO:0000269|PubMed:27458237, ECO:0000269|PubMed:27545878, ECO:0000269|PubMed:27591049}.
• Pathway: Necroptosis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.263
• rvis_EVS: -0.86
• rvis_percentile_EVS: 10.85

Haploinsufficiency Scores

• pHI: 0.329
• hipred: Y
• hipred_score: 0.690
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.917

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata2
• Phenotype: reproductive system phenotype; cellular phenotype; immune system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;regulation of tumor necrosis factor-mediated signaling pathway;programmed cell death;regulation of inflammatory response;regulation of necroptotic process;protein K63-linked deubiquitination;protein linear deubiquitination
• Cellular component: fibrillar center;nucleus;cytoplasm
• Molecular function: molecular_function;protein binding