SPATA48

spermatogenesis associated 48

Basic information

Region (hg38): 7:50095882-50159256

Previous symbols: [ "C7orf72" ]

Links

ENSG00000164500 ∙ NCBI:100130988 ∙ ∙ HGNC:22564 ∙ Uniprot:A4D263 ∙ 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 SPATA48 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA48 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in SPATA48

This is a list of pathogenic ClinVar variants found in the SPATA48 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-50096135-G-A		not specified	Uncertain significance (Sep 17, 2021)
7-50104347-A-C		not specified	Uncertain significance (Aug 04, 2021)
7-50134227-G-A		not specified	Uncertain significance (Jun 11, 2021)
7-50141340-C-T		not specified	Uncertain significance (Nov 09, 2021)
7-50141370-T-C		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA48	protein_coding	protein_coding	ENST00000297001	9	63795

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.77e-8	0.351	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.710	185	214	0.863	0.0000105	2847
Missense in Polyphen		57	66.41	0.85831		850
Synonymous	1.63	56	73.8	0.759	0.00000349	849
Loss of Function	0.688	13	16.0	0.814	7.35e-7	252

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: 1.17
• rvis_percentile_EVS: 92.68

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Spata48

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function