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.

• not_specified (11 variants)

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. These statistics are base on transcript: NM_001024601.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			10	1		11
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	10	1	0

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