SP2

Sp2 transcription factor, the group of Sp transcription factors|Zinc fingers C2H2-type

Basic information

Region (hg38): 17:47896150-47928957

Links

ENSG00000167182 ∙ NCBI:6668 ∙ OMIM:601801 ∙ HGNC:11207 ∙ Uniprot:Q02086 ∙ 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 SP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SP2 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				2		2
missense			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	2	0

Variants in SP2

This is a list of pathogenic ClinVar variants found in the SP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-47916235-C-G		not specified	Uncertain significance (Mar 02, 2023)
17-47916238-C-T		not specified	Uncertain significance (Jun 01, 2023)
17-47916420-C-T		not specified	Uncertain significance (Dec 21, 2022)
17-47916459-A-G		not specified	Uncertain significance (Sep 15, 2021)
17-47916570-A-G		not specified	Uncertain significance (Jan 30, 2024)
17-47916631-C-T		not specified	Uncertain significance (Nov 08, 2022)
17-47916637-C-T		not specified	Uncertain significance (Jan 02, 2024)
17-47916650-C-T			Likely benign (Jun 01, 2022)
17-47916660-G-A		not specified	Uncertain significance (Nov 10, 2022)
17-47916672-G-C		not specified	Uncertain significance (Jun 03, 2022)
17-47916693-G-A		not specified	Uncertain significance (Dec 01, 2023)
17-47916703-C-T		not specified	Uncertain significance (Apr 23, 2024)
17-47916747-G-A		not specified	Uncertain significance (May 18, 2022)
17-47916761-G-C		not specified	Uncertain significance (Nov 27, 2023)
17-47916784-C-A		not specified	Uncertain significance (Apr 17, 2023)
17-47916894-G-A		not specified	Uncertain significance (Oct 26, 2021)
17-47916898-A-G		not specified	Uncertain significance (Nov 30, 2022)
17-47916901-T-A		not specified	Uncertain significance (Nov 23, 2021)
17-47916948-G-A		not specified	Uncertain significance (Nov 07, 2023)
17-47917025-G-C		not specified	Uncertain significance (Nov 18, 2022)
17-47917036-G-A		not specified	Uncertain significance (Nov 18, 2022)
17-47922975-C-T		not specified	Uncertain significance (Oct 25, 2022)
17-47922988-G-C		not specified	Uncertain significance (May 09, 2023)
17-47923080-A-G		not specified	Uncertain significance (Apr 19, 2024)
17-47923247-G-A		not specified	Uncertain significance (Mar 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SP2	protein_coding	protein_coding	ENST00000376741	7	32808

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00279	124803	0	2	124805	0.00000801

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.37	247	376	0.656	0.0000227	3962
Missense in Polyphen		50	102.59	0.4874		1128
Synonymous	-0.715	172	160	1.07	0.0000103	1321
Loss of Function	4.12	1	21.7	0.0461	0.00000112	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.00000885	0.00000885
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites.

Recessive Scores

• pRec: 0.287

Intolerance Scores

• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.28

Haploinsufficiency Scores

• pHI: 0.951
• hipred: Y
• hipred_score: 0.617
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sp2
• Phenotype: growth/size/body region phenotype; cellular phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); normal 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); embryo phenotype

Zebrafish Information Network

• Gene name: sp2
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;immune response;multicellular organism growth
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;protein binding;histone deacetylase binding;metal ion binding