SPATA45

spermatogenesis associated 45

Basic information

Region (hg38): 1:212830141-212847649

Previous symbols: [ "C1orf227" ]

Links

ENSG00000185523 ∙ NCBI:149643 ∙ ∙ HGNC:33709 ∙ Uniprot:Q537H7 ∙ 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 SPATA45 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA45 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in SPATA45

This is a list of pathogenic ClinVar variants found in the SPATA45 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-212835879-G-A		not specified	Uncertain significance (Dec 27, 2023)
1-212835891-T-C		not specified	Uncertain significance (Aug 08, 2023)
1-212835903-G-A		not specified	Uncertain significance (Feb 25, 2025)
1-212835950-A-G		not specified	Uncertain significance (May 26, 2024)
1-212835996-G-A		not specified	Likely benign (Feb 21, 2024)
1-212836040-C-T		not specified	Uncertain significance (Nov 06, 2023)
1-212836044-C-T		not specified	Uncertain significance (Jun 11, 2021)
1-212836078-C-A		not specified	Uncertain significance (Jan 15, 2025)
1-212836130-G-A		not specified	Uncertain significance (Mar 26, 2024)
1-212836130-G-T		not specified	Uncertain significance (Jun 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA45	protein_coding	protein_coding	ENST00000332912	2	17509

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.198	0.659	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.401	43	51.1	0.842	0.00000240	656
Missense in Polyphen		0	1.5933	0		19
Synonymous	-1.38	25	17.6	1.42	8.42e-7	176
Loss of Function	0.978	1	2.75	0.364	1.15e-7	40

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: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Spata45