SIVA1

SIVA1 apoptosis inducing factor

Basic information

Region (hg38): 14:104753147-104768494

Links

ENSG00000184990 ∙ NCBI:10572 ∙ OMIM:605567 ∙ HGNC:17712 ∙ Uniprot:O15304 ∙ 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 SIVA1 gene.

• not_specified (38 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIVA1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006427.4. 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			36	2	1	39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	36	2	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIVA1	protein_coding	protein_coding	ENST00000329967	4	15395

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0257	0.924	125730	0	7	125737	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00676	114	114	0.998	0.00000709	1109
Missense in Polyphen		31	40.58	0.76392		438
Synonymous	-0.654	59	52.9	1.11	0.00000372	367
Loss of Function	1.68	4	9.61	0.416	6.64e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Induces CD27-mediated apoptosis. Inhibits BCL2L1 isoform Bcl-x(L) anti-apoptotic activity. Inhibits activation of NF-kappa- B and promotes T-cell receptor-mediated apoptosis. {ECO:0000269|PubMed:12011449, ECO:0000269|PubMed:14739602, ECO:0000269|PubMed:15034012, ECO:0000269|PubMed:15958577, ECO:0000269|PubMed:16491128}.

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.149
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.18

Haploinsufficiency Scores

• pHI: 0.158
• hipred: Y
• hipred_score: 0.508
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.805

Mouse Genome Informatics

• Gene name: Siva1
• Phenotype: immune system phenotype; neoplasm; hematopoietic system phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype

Gene ontology

• Biological process: viral entry into host cell;extrinsic apoptotic signaling pathway
• Cellular component: nucleoplasm;cytoplasm
• Molecular function: virus receptor activity;tumor necrosis factor receptor binding;CD27 receptor binding;protein binding;metal ion binding