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 (436 variants)
• Inborn_genetic_diseases (101 variants)
• not_provided (24 variants)
• Mycobacterium_tuberculosis,_susceptibility_to (15 variants)
• SP110-related_disorder (13 variants)
• not_specified (3 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. These statistics are base on transcript: NM_000080424.4. 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			3	97	5	105
missense	1		224	19	4	248
nonsense	4	7	1	1		13
start loss			1			1
frameshift	13	5	3			21
splice donor/acceptor (+/-2bp)		7	3			10
Total	18	19	235	117	9

Highest pathogenic variant AF is 0.000114628165

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