SPATA20

spermatogenesis associated 20

Basic information

Region (hg38): 17:50543058-50555852

Links

ENSG00000006282 ∙ NCBI:64847 ∙ OMIM:613939 ∙ HGNC:26125 ∙ Uniprot:Q8TB22 ∙ 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 SPATA20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA20 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						0
missense			62	3		65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	62	3	0

Variants in SPATA20

This is a list of pathogenic ClinVar variants found in the SPATA20 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-50547221-C-T		not specified	Uncertain significance (Oct 26, 2021)
17-50547222-G-C		not specified	Uncertain significance (Jul 20, 2021)
17-50547231-T-C		not specified	Uncertain significance (Oct 12, 2022)
17-50547242-C-T		not specified	Uncertain significance (Feb 12, 2024)
17-50548312-G-A		not specified	Uncertain significance (Apr 13, 2022)
17-50548390-C-T		not specified	Uncertain significance (Oct 12, 2021)
17-50548395-C-T		not specified	Uncertain significance (Mar 21, 2024)
17-50548405-A-G		not specified	Uncertain significance (Mar 07, 2023)
17-50548406-C-G		not specified	Uncertain significance (Dec 28, 2022)
17-50548438-A-G		not specified	Uncertain significance (Jul 09, 2021)
17-50548440-A-G			Likely benign (Jan 01, 2024)
17-50548816-A-G		not specified	Uncertain significance (Jun 21, 2022)
17-50548873-T-C		not specified	Uncertain significance (Jun 21, 2021)
17-50548878-C-T		not specified	Uncertain significance (Mar 22, 2022)
17-50548927-G-A		not specified	Uncertain significance (Aug 02, 2023)
17-50548959-G-A		not specified	Uncertain significance (Feb 21, 2024)
17-50549049-A-G		not specified	Uncertain significance (Jun 03, 2024)
17-50549058-G-A		not specified	Uncertain significance (Jun 01, 2023)
17-50549326-G-A		not specified	Uncertain significance (Jul 30, 2023)
17-50549350-G-A		not specified	Uncertain significance (Feb 16, 2023)
17-50549367-G-A		not specified	Uncertain significance (Jun 21, 2021)
17-50549394-G-A		not specified	Uncertain significance (Jun 16, 2023)
17-50549410-G-A		not specified	Uncertain significance (Aug 12, 2021)
17-50549427-G-C		not specified	Uncertain significance (May 16, 2024)
17-50549434-G-T		not specified	Uncertain significance (May 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA20	protein_coding	protein_coding	ENST00000006658	17	12795

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.99e-9	1.00	125515	0	233	125748	0.000927

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.123	490	498	0.985	0.0000326	5156
Missense in Polyphen		154	164.39	0.93681		1727
Synonymous	0.417	200	208	0.963	0.0000136	1644
Loss of Function	3.18	22	45.0	0.489	0.00000244	456

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00869	0.00860
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000563	0.000554
Middle Eastern	0.000218	0.000217
South Asian	0.000294	0.000294
Other	0.000660	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in fertility regulation. {ECO:0000250}.

Recessive Scores

• pRec: 0.155

Intolerance Scores

• loftool: 0.722
• rvis_EVS: -0.59
• rvis_percentile_EVS: 18.26

Haploinsufficiency Scores

• pHI: 0.148
• hipred: N
• hipred_score: 0.426
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.517

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata20
• Phenotype: reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;cell differentiation
• Cellular component: extracellular region
• Molecular function: catalytic activity