SPATA1

spermatogenesis associated 1

Basic information

Region (hg38): 1:84506300-84567379

Links

ENSG00000122432 ∙ NCBI:100505741 ∙ ∙ HGNC:14682 ∙ Uniprot:Q5VX52 ∙ 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 SPATA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA1 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			15	3	2	20
Total	0	0	15	3	2

Variants in SPATA1

This is a list of pathogenic ClinVar variants found in the SPATA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-84555066-T-C		not specified	Uncertain significance (Jan 10, 2023)
1-84555086-G-A			Benign (Sep 12, 2017)
1-84555111-C-T		not specified	Uncertain significance (Feb 14, 2025)
1-84555112-G-A			Benign (Nov 27, 2017)
1-84555159-G-C		not specified	Uncertain significance (Apr 09, 2024)
1-84563336-G-A		not specified	Likely benign (Feb 07, 2025)
1-84563349-C-T		not specified	Uncertain significance (May 18, 2022)
1-84563354-C-T		not specified	Likely benign (Oct 29, 2024)
1-84563355-G-A		not specified	Uncertain significance (Apr 07, 2023)
1-84563364-C-T		not specified	Uncertain significance (Feb 18, 2025)
1-84563384-C-T		not specified	Uncertain significance (Nov 07, 2024)
1-84563387-A-G		not specified	Uncertain significance (Nov 03, 2022)
1-84563402-A-G			Likely benign (Nov 01, 2022)
1-84563412-C-T		not specified	Uncertain significance (Oct 01, 2024)
1-84563415-G-C		not specified	Uncertain significance (Apr 13, 2023)
1-84563754-G-T		not specified	Uncertain significance (Apr 22, 2022)
1-84563791-G-A		not specified	Uncertain significance (Jan 03, 2024)
1-84563810-C-T		not specified	Likely benign (Nov 10, 2024)
1-84563814-T-C		not specified	Uncertain significance (May 26, 2022)
1-84565843-G-A		not specified	Uncertain significance (Sep 30, 2024)
1-84565843-G-T		not specified	Uncertain significance (Jan 23, 2024)
1-84565921-A-G		not specified	Uncertain significance (Mar 20, 2024)
1-84565973-T-C		not specified	Uncertain significance (Dec 11, 2024)
1-84565993-C-G		not specified	Uncertain significance (Nov 12, 2024)
1-84566002-T-A		not specified	Uncertain significance (Jan 19, 2025)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Haploinsufficiency Scores

• pHI: 0.104

Mouse Genome Informatics

• Gene name: Spata1