SP140

SP140 nuclear body protein, the group of PHD finger proteins|Bromodomain containing

Basic information

Region (hg38): 2:230203109-230313215

Links

ENSG00000079263 ∙ NCBI:11262 ∙ OMIM:608602 ∙ HGNC:17133 ∙ Uniprot:Q13342 ∙ 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 SP140 gene.

• Inborn genetic diseases (25 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SP140 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	2	3
missense			20	5	2	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	20	6	4

Variants in SP140

This is a list of pathogenic ClinVar variants found in the SP140 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-230207972-T-C		Hepatic veno-occlusive disease-immunodeficiency syndrome	Likely benign (Nov 19, 2023)
2-230207977-T-C		Hepatic veno-occlusive disease-immunodeficiency syndrome	Conflicting classifications of pathogenicity (Oct 11, 2023)
2-230207990-C-T			Uncertain significance (May 24, 2019)
2-230207994-C-T		Hepatic veno-occlusive disease-immunodeficiency syndrome • not specified	Benign (Feb 01, 2024)
2-230208002-CT-C		Hepatic veno-occlusive disease-immunodeficiency syndrome	Pathogenic (Nov 01, 2022)
2-230208009-T-C		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Nov 01, 2022)
2-230208012-T-A		Hepatic veno-occlusive disease-immunodeficiency syndrome	Likely pathogenic (Jan 27, 2014)
2-230208012-T-C		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Aug 15, 2022)
2-230208022-T-C		Hepatic veno-occlusive disease-immunodeficiency syndrome	Likely benign (Jun 20, 2023)
2-230208041-C-A		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Apr 08, 2022)
2-230208041-C-G		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Aug 30, 2021)
2-230208047-T-C		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Jul 19, 2022)
2-230208057-T-C		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Jan 03, 2023)
2-230208057-T-G		Inborn genetic diseases	Uncertain significance (Dec 12, 2023)
2-230208071-G-T		Hepatic veno-occlusive disease-immunodeficiency syndrome	Likely benign (Oct 14, 2023)
2-230208078-GT-G		Hepatic veno-occlusive disease-immunodeficiency syndrome	Benign (Jun 26, 2022)
2-230209916-A-G		Hepatic veno-occlusive disease-immunodeficiency syndrome	Conflicting classifications of pathogenicity (Apr 30, 2023)
2-230209917-A-G		Hepatic veno-occlusive disease-immunodeficiency syndrome	Likely benign (Mar 04, 2023)
2-230209921-C-T		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Jan 12, 2018)
2-230209934-T-C		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Oct 17, 2022)
2-230209946-G-T		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (May 13, 2022)
2-230209958-C-A		Hepatic veno-occlusive disease-immunodeficiency syndrome	Uncertain significance (Dec 08, 2021)
2-230209980-A-G		Hepatic veno-occlusive disease-immunodeficiency syndrome	Likely benign (Jul 26, 2022)
2-230210007-C-G		Inborn genetic diseases	Uncertain significance (Jun 21, 2023)
2-230210491-G-A		Mycobacterium tuberculosis, susceptibility to	Uncertain significance (Apr 01, 2007)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SP140	protein_coding	protein_coding	ENST00000392045	27	155937

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.00e-8	1.00	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.787	407	454	0.896	0.0000228	5738
Missense in Polyphen		93	134.63	0.69077		1838
Synonymous	1.12	146	164	0.889	0.00000920	1494
Loss of Function	4.00	22	53.6	0.410	0.00000254	688

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000443	0.000427
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.000112	0.000109
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the nuclear body, also known as nuclear domain 10, PML oncogenic domain, and KR body (PubMed:8910577). May be involved in the pathogenesis of acute promyelocytic leukemia and viral infection (PubMed:8910577). May play a role in chromatin-mediated regulation of gene expression although it does not bind to histone H3 tails (PubMed:24267382). {ECO:0000269|PubMed:24267382, ECO:0000269|PubMed:8910577, ECO:0000303|PubMed:8910577}.

Recessive Scores

• pRec: 0.0622

Intolerance Scores

• loftool: 0.699
• rvis_EVS: 0.32
• rvis_percentile_EVS: 72.8

Haploinsufficiency Scores

• pHI: 0.0278
• hipred: N
• hipred_score: 0.214
• ghis: 0.479

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.730

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sp140

Gene ontology

• Biological process: regulation of transcription, DNA-templated;defense response
• Cellular component: fibrillar center;nucleus;nuclear envelope;nucleoplasm;mitochondrion;PML body
• Molecular function: DNA binding;DNA-binding transcription factor activity;protein binding;metal ion binding