SP3

Sp3 transcription factor, the group of Zinc fingers C2H2-type|Sp transcription factors

Basic information

Region (hg38): 2:173880850-173965373

Links

ENSG00000172845 ∙ NCBI:6670 ∙ OMIM:601804 ∙ HGNC:11208 ∙ Uniprot:Q02447 ∙ 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 SP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SP3 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					3	3
missense			48	1	1	50
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	49	1	4

Variants in SP3

This is a list of pathogenic ClinVar variants found in the SP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-173909949-T-C		not specified	Uncertain significance (Jul 14, 2021)
2-173910005-A-G		not specified	Uncertain significance (Mar 01, 2023)
2-173910024-C-T		not specified	Likely benign (Aug 30, 2022)
2-173910041-C-T		not specified	Uncertain significance (Jul 05, 2024)
2-173910047-C-T		not specified	Uncertain significance (Sep 27, 2021)
2-173910061-T-G		not specified	Uncertain significance (Oct 05, 2023)
2-173910099-C-A		not specified	Uncertain significance (Jul 12, 2022)
2-173910110-G-A		not specified	Uncertain significance (Jan 10, 2025)
2-173910145-T-G			Benign (May 14, 2018)
2-173910181-TG-T		See cases	Uncertain significance (Aug 08, 2019)
2-173910188-A-G		not specified	Uncertain significance (Dec 08, 2023)
2-173913129-T-C		not specified	Uncertain significance (Oct 01, 2024)
2-173913214-C-T		not specified	Uncertain significance (Nov 10, 2024)
2-173918651-C-T		not specified	Uncertain significance (Nov 18, 2023)
2-173918653-T-C		not specified	Uncertain significance (Jun 06, 2023)
2-173918700-G-A			Benign (Jun 18, 2018)
2-173918742-C-G		not specified	Uncertain significance (Jan 24, 2024)
2-173954927-T-C		not specified	Uncertain significance (Mar 11, 2022)
2-173954927-T-G		not specified	Uncertain significance (Jul 11, 2023)
2-173954938-G-C		not specified	Uncertain significance (Jan 17, 2025)
2-173954946-T-C			Benign (May 14, 2018)
2-173954968-G-C		not specified	Uncertain significance (Aug 05, 2024)
2-173955020-C-G		not specified	Uncertain significance (May 09, 2023)
2-173955062-C-A		not specified	Uncertain significance (Dec 04, 2024)
2-173955068-T-C		not specified	Uncertain significance (Jan 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SP3	protein_coding	protein_coding	ENST00000310015	7	59244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000504	125729	0	2	125731	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.63	309	401	0.771	0.0000199	5033
Missense in Polyphen		80	145.7	0.54906		1900
Synonymous	-2.82	192	148	1.29	0.00000781	1618
Loss of Function	5.11	1	32.4	0.0308	0.00000164	351

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000964	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional factor that can act as an activator or repressor depending on isoform and/or post-translational modifications. Binds to GT and GC boxes promoter elements. Competes with SP1 for the GC-box promoters. Weak activator of transcription but can activate a number of genes involved in different processes such as cell-cycle regulation, hormone- induction and house-keeping. {ECO:0000269|PubMed:10391891, ECO:0000269|PubMed:11812829, ECO:0000269|PubMed:12419227, ECO:0000269|PubMed:12837748, ECO:0000269|PubMed:15247228, ECO:0000269|PubMed:15494207, ECO:0000269|PubMed:15554904, ECO:0000269|PubMed:16781829, ECO:0000269|PubMed:17548428, ECO:0000269|PubMed:18187045, ECO:0000269|PubMed:18617891, ECO:0000269|PubMed:9278495}.
• Pathway: Selenium Metabolism and Selenoproteins;MECP2 and Associated Rett Syndrome;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;overview of telomerase rna component gene hterc transcriptional regulation;effects of calcineurin in keratinocyte differentiation;SUMOylation of transcription factors;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;SUMOylation;Regulation of Telomerase;Regulation of nuclear SMAD2/3 signaling (Consensus)

Recessive Scores

• pRec: 0.191

Intolerance Scores

• loftool: 0.122
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.69

Haploinsufficiency Scores

• pHI: 0.963
• hipred: Y
• hipred_score: 0.825
• ghis: 0.587

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.339

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sp3
• Phenotype: limbs/digits/tail phenotype; vision/eye phenotype; immune system phenotype; skeleton phenotype; embryo phenotype; respiratory system phenotype; liver/biliary system 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); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); endocrine/exocrine gland phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;ossification;natural killer cell differentiation;trophectodermal cell differentiation;liver development;embryonic placenta development;regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;B cell differentiation;T cell differentiation;megakaryocyte differentiation;monocyte differentiation;lung development;granulocyte differentiation;enucleate erythrocyte differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;embryonic camera-type eye morphogenesis;embryonic skeletal system development;embryonic process involved in female pregnancy;definitive hemopoiesis
• Cellular component: nucleus;nucleoplasm;PML body;transcriptional repressor complex;protein-DNA complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;proximal promoter sequence-specific DNA binding;DNA-binding transcription repressor activity, RNA polymerase II-specific;chromatin binding;protein binding;metal ion binding