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.

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.

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			14	1	1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	1

Variants in SIVA1

This is a list of pathogenic ClinVar variants found in the SIVA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-104753218-G-A		not specified	Uncertain significance (May 12, 2024)
14-104753238-C-A		not specified	Uncertain significance (Aug 28, 2023)
14-104753244-C-A		not specified	Uncertain significance (Apr 11, 2023)
14-104753244-C-G		not specified	Uncertain significance (Jun 10, 2022)
14-104753269-G-A		not specified	Likely benign (Sep 29, 2022)
14-104753271-G-A		not specified	Uncertain significance (Oct 26, 2021)
14-104755660-C-T		not specified	Uncertain significance (Jun 10, 2022)
14-104755701-G-A		not specified	Likely benign (Jun 20, 2024)
14-104755728-C-T		not specified	Uncertain significance (Aug 17, 2021)
14-104755743-G-T		not specified	Uncertain significance (Mar 31, 2024)
14-104755779-C-G		not specified	Uncertain significance (Dec 07, 2021)
14-104755788-C-T		not specified	Uncertain significance (Feb 05, 2024)
14-104755789-G-A		not specified	Uncertain significance (Nov 09, 2021)
14-104756615-G-T		not specified	Uncertain significance (Jan 20, 2023)
14-104756624-A-G		not specified	Uncertain significance (Dec 16, 2023)
14-104756712-C-G			Benign (Nov 15, 2018)
14-104756732-G-A		not specified	Uncertain significance (Dec 16, 2022)
14-104759439-T-A		not specified	Uncertain significance (Jun 03, 2022)

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