SP100

SP100 nuclear antigen, the group of PHD finger proteins|Bromodomain containing

Basic information

Region (hg38): 2:230415941-230545606

Links

ENSG00000067066 ∙ NCBI:6672 ∙ OMIM:604585 ∙ HGNC:11206 ∙ Uniprot:P23497 ∙ 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 SP100 gene.

• Inborn genetic diseases (26 variants)
• not provided (2 variants)
• Hereditary breast ovarian cancer syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SP100 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	1
missense			24	3		27
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	3	1

Variants in SP100

This is a list of pathogenic ClinVar variants found in the SP100 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-230416310-G-T		not specified	Uncertain significance (Sep 16, 2021)
2-230442991-C-A		not specified	Uncertain significance (Dec 20, 2023)
2-230443038-A-C		not specified	Uncertain significance (Sep 26, 2022)
2-230444191-C-G		not specified	Uncertain significance (Mar 12, 2024)
2-230444289-G-A		not specified	Uncertain significance (Dec 09, 2023)
2-230444331-A-G		not specified	Likely benign (Dec 07, 2021)
2-230446855-A-G		not specified	Likely benign (Dec 09, 2023)
2-230446869-G-A		not specified	Uncertain significance (Mar 27, 2023)
2-230449091-C-T		not specified	Uncertain significance (Feb 06, 2023)
2-230449109-G-A		not specified	Likely benign (May 18, 2022)
2-230449564-C-A		not specified	Uncertain significance (Dec 19, 2022)
2-230449570-C-T		not specified	Uncertain significance (Jun 24, 2022)
2-230450179-C-G		not specified	Uncertain significance (Aug 08, 2022)
2-230461316-G-A			Likely benign (Jan 05, 2018)
2-230461336-G-A		not specified	Uncertain significance (Dec 09, 2023)
2-230461378-G-C		not specified	Uncertain significance (Feb 28, 2024)
2-230461379-C-A		not specified	Uncertain significance (Apr 04, 2023)
2-230462459-G-A		not specified	Likely benign (Nov 28, 2023)
2-230462469-C-T			Benign (Jul 29, 2018)
2-230464096-A-G		not specified	Uncertain significance (Aug 04, 2023)
2-230464133-G-A		not specified	Uncertain significance (Aug 10, 2021)
2-230467165-C-T		not specified	Uncertain significance (Jun 24, 2022)
2-230467170-G-A		not specified	Uncertain significance (Oct 20, 2023)
2-230470015-G-T		not specified	Uncertain significance (Nov 06, 2023)
2-230470057-A-C		not specified	Uncertain significance (Sep 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SP100	protein_coding	protein_coding	ENST00000340126	29	128149

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.76e-12	1.00	125193	2	551	125746	0.00220

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.597	426	462	0.922	0.0000231	5911
Missense in Polyphen		56	54.733	1.0231		587
Synonymous	1.42	141	164	0.859	0.00000892	1501
Loss of Function	3.55	29	58.3	0.498	0.00000299	707

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00341	0.00341
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000109
Finnish	0.00213	0.00208
European (Non-Finnish)	0.00365	0.00363
Middle Eastern	0.000113	0.000109
South Asian	0.0000694	0.0000653
Other	0.00245	0.00245

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Together with PML, this tumor suppressor is a major constituent of the PML bodies, a subnuclear organelle involved in a large number of physiological processes including cell growth, differentiation and apoptosis. Functions as a transcriptional coactivator of ETS1 and ETS2 according to PubMed:11909962. Under certain conditions, it may also act as a corepressor of ETS1 preventing its binding to DNA according to PubMed:15247905. Through the regulation of ETS1 it may play a role in angiogenesis, controlling endothelial cell motility and invasion. Through interaction with the MRN complex it may be involved in the regulation of telomeres lengthening. May also regulate TP53- mediated transcription and through CASP8AP2, regulate FAS-mediated apoptosis. Also plays a role in infection by viruses, including human cytomegalovirus and Epstein-Barr virus, through mechanisms that may involve chromatin and/or transcriptional regulation. {ECO:0000269|PubMed:11909962, ECO:0000269|PubMed:14647468, ECO:0000269|PubMed:15247905, ECO:0000269|PubMed:15592518, ECO:0000269|PubMed:15767676, ECO:0000269|PubMed:16177824, ECO:0000269|PubMed:17245429, ECO:0000269|PubMed:21274506, ECO:0000269|PubMed:21880768}.
• Pathway: Viral carcinogenesis - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Cytokine Signaling in Immune system;SUMOylation of DNA damage response and repair proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;Immune System;SUMOylation;regulation of transcriptional activity by pml;Interferon gamma signaling;Interferon Signaling (Consensus)

Intolerance Scores

• loftool: 0.494
• rvis_EVS: 0.23
• rvis_percentile_EVS: 68.57

Haploinsufficiency Scores

• pHI: 0.763
• hipred: Y
• hipred_score: 0.622
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.978

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sp100

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;telomere maintenance;DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator;negative regulation of endothelial cell migration;viral process;response to type I interferon;response to interferon-gamma;negative regulation of DNA binding;negative regulation of DNA-binding transcription factor activity;maintenance of protein location;regulation of angiogenesis;positive regulation of transcription, DNA-templated;negative regulation of protein export from nucleus;negative regulation of cellular component movement;interferon-gamma-mediated signaling pathway;type I interferon signaling pathway;regulation of extrinsic apoptotic signaling pathway via death domain receptors;regulation of Fas signaling pathway
• Cellular component: nuclear chromosome, telomeric region;nucleus;nucleoplasm;cytoplasm;nuclear body;PML body;Mre11 complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;kinase binding;protein domain specific binding;protein dimerization activity;chromo shadow domain binding