SPATA46

spermatogenesis associated 46

Basic information

Region (hg38): 1:162373203-162376854

Previous symbols: [ "C1orf111" ]

Links

ENSG00000171722 ∙ NCBI:284680 ∙ OMIM:617257 ∙ HGNC:27648 ∙ Uniprot:Q5T0L3 ∙ 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 SPATA46 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA46 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 SPATA46

This is a list of pathogenic ClinVar variants found in the SPATA46 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-162374076-A-G		not specified	Uncertain significance (Aug 10, 2021)
1-162374359-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-162374415-G-A		not specified	Uncertain significance (Jul 15, 2021)
1-162374416-A-C		not specified	Uncertain significance (Aug 10, 2021)
1-162374512-C-T		not specified	Uncertain significance (Aug 12, 2021)
1-162374542-G-A		not specified	Uncertain significance (Aug 09, 2021)
1-162374557-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-162376739-C-T		not specified	Likely benign (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA46	protein_coding	protein_coding	ENST00000367935	3	3668

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.77e-10	0.0176	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0723	153	151	1.02	0.00000809	1724
Missense in Polyphen		45	45.831	0.98186		551
Synonymous	0.0688	58	58.7	0.989	0.00000315	501
Loss of Function	-1.01	13	9.62	1.35	4.76e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000394	0.000394
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000109	0.000109
South Asian	0.000653	0.000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Play a role in spermiogenesis and fertilization. {ECO:0000250|UniProtKB:Q4FZF2}.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.06

Haploinsufficiency Scores

• pHI: 0.279
• hipred: N
• hipred_score: 0.146
• ghis: 0.408

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Spata46

Gene ontology

• Biological process: spermatogenesis;fusion of sperm to egg plasma membrane involved in single fertilization;cell differentiation
• Cellular component: nuclear membrane
• Molecular function: protein binding