SP110

SP110 nuclear body protein, the group of PHD finger proteins|Minor histocompatibility antigens|Bromodomain containing

Basic information

Region (hg38): 2:230165186-230225729

Previous symbols: [ "IFI41", "IFI75" ]

Links

ENSG00000135899 ∙ NCBI:3431 ∙ OMIM:604457 ∙ HGNC:5401 ∙ Uniprot:Q9HB58 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hepatic veno-occlusive disease-immunodeficiency syndrome (Moderate), mode of inheritance: AR
• hepatic veno-occlusive disease-immunodeficiency syndrome (Supportive), mode of inheritance: AR
• hepatic veno-occlusive disease-immunodeficiency syndrome (Strong), mode of inheritance: AR
• hepatic veno-occlusive disease-immunodeficiency syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hepatic venoocclusive disease with immunodeficiency	AR	Allergy/Immunology/Infectious	Mortality is high if the condition is unrecognized; interventions include intravenous immunoglobulin and infectious prophylaxis (Pneumocystis jerovici)	Allergy/Immunology/Infectious; Cardiovascular; Gastrointestinal; Neurologic	16648851; 17510920; 22621957; 22982295

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SP110 gene.

• Hepatic veno-occlusive disease-immunodeficiency syndrome (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SP110 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			1	76	7	84
missense			193	11	10	214
nonsense	6	4	1			11
start loss			1			1
frameshift	14	2	2			18
inframe indel			2			2
splice donor/acceptor (+/-2bp)		4	2			6
splice region			11	8		19
non coding			11	51	12	74
Total	20	10	213	138	29

Highest pathogenic variant AF is 0.0000658

Variants in SP110

This is a list of pathogenic ClinVar variants found in the SP110 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-230168917-AT-A		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Jun 14, 2016)
2-230168917-A-ATTAATT		Hepatic veno-occlusive disease-immunodeficiency syndrome	Benign (Jun 14, 2016)
2-230168920-T-A		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Jan 12, 2018)
2-230168921-T-A		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Jan 12, 2018)
2-230168966-G-T		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Jan 13, 2018)
2-230169042-C-T		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Jan 12, 2018)
2-230169128-G-C		Hepatic veno-occlusive disease-immunodeficiency syndrome • Inborn genetic diseases	Uncertain significance (Aug 01, 2024)
2-230169131-A-C		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Sep 27, 2021)
2-230169139-G-C		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Jan 12, 2023)
2-230169144-C-G		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Oct 17, 2022)
2-230169144-C-T		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Dec 13, 2021)
2-230169146-C-T		Hepatic veno-occlusive disease-immunodeficiency syndrome • Mycobacterium tuberculosis, susceptibility to;Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Mar 30, 2021)
2-230169147-C-A		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Sep 02, 2021)
2-230169148-G-A		Hepatic veno-occlusive disease-immunodeficiency syndrome	Likely benign (Feb 11, 2020)
2-230169150-C-T		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Jun 30, 2022)
2-230169152-T-C		Hepatic veno-occlusive disease-immunodeficiency syndrome • Inborn genetic diseases	Conflicting classifications of pathogenicity (Mar 24, 2023)
2-230169154-G-A		Hepatic veno-occlusive disease-immunodeficiency syndrome	Likely benign (Sep 12, 2023)
2-230169160-A-G		Hepatic veno-occlusive disease-immunodeficiency syndrome	Likely benign (Apr 29, 2022)
2-230169166-A-G		Hepatic veno-occlusive disease-immunodeficiency syndrome • SP110-related disorder	Likely benign (Mar 14, 2023)
2-230169167-C-T		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Aug 09, 2022)
2-230169168-C-T		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Sep 01, 2021)
2-230169169-G-A		Hepatic veno-occlusive disease-immunodeficiency syndrome	Likely benign (Jun 08, 2022)
2-230169171-G-A		Inborn genetic diseases	Likely benign (Sep 06, 2022)
2-230169174-C-T		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Oct 31, 2018)
2-230169175-G-A		Hepatic veno-occlusive disease-immunodeficiency syndrome	Likely benign (Oct 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SP110	protein_coding	protein_coding	ENST00000258381	18	58436

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.46e-14	0.745	125659	0	89	125748	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.335	355	373	0.951	0.0000208	4695
Missense in Polyphen		24	23.936	1.0027		232
Synonymous	-0.121	141	139	1.01	0.00000863	1307
Loss of Function	1.83	28	40.6	0.689	0.00000221	493

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000420	0.000420
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000220	0.000220
Middle Eastern	0.000109	0.000109
South Asian	0.00160	0.00160
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor. May be a nuclear hormone receptor coactivator. Enhances transcription of genes with retinoic acid response elements (RARE).
• Disease: DISEASE: Hepatic venoocclusive disease with immunodeficiency (VODI) [MIM:235550]: Autosomal recessive primary immunodeficiency associated with hepatic vascular occlusion and fibrosis. The immunodeficiency is characterized by severe hypogammaglobulinemia, combined T and B-cell immunodeficiency, absent lymph node germinal centers, and absent tissue plasma cells. {ECO:0000269|PubMed:16648851}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• loftool: 0.496
• rvis_EVS: 0.54
• rvis_percentile_EVS: 81.1

Haploinsufficiency Scores

• pHI: 0.0394
• hipred: N
• hipred_score: 0.214
• ghis: 0.450

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.682

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sp110

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;viral process
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding