SP4

Sp4 transcription factor, the group of Sp transcription factors|Zinc fingers C2H2-type|MicroRNA protein coding host genes

Basic information

Region (hg38): 7:21428042-21514822

Links

ENSG00000105866 ∙ NCBI:6671 ∙ OMIM:600540 ∙ HGNC:11209 ∙ Uniprot:Q02446 ∙ 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 SP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SP4 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						0
missense			43	2	1	46
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	2	1

Variants in SP4

This is a list of pathogenic ClinVar variants found in the SP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-21428701-A-C		not specified	Uncertain significance (Nov 10, 2022)
7-21428754-G-A		not specified	Uncertain significance (Aug 22, 2023)
7-21428754-G-C		not specified	Uncertain significance (May 23, 2023)
7-21428758-A-AT		6 conditions	Uncertain significance (Mar 24, 2023)
7-21428764-A-G		not specified	Uncertain significance (May 24, 2024)
7-21429423-A-T		not specified	Uncertain significance (Jun 29, 2022)
7-21429442-G-T		not specified	Uncertain significance (Jun 28, 2022)
7-21429484-T-A		not specified	Uncertain significance (May 17, 2023)
7-21429491-C-T		not specified	Uncertain significance (Dec 03, 2021)
7-21429527-C-T		not specified	Uncertain significance (May 17, 2023)
7-21429536-C-T		not specified	Uncertain significance (Apr 14, 2022)
7-21429568-G-A		not specified	Uncertain significance (Apr 19, 2023)
7-21429588-AT-A			Uncertain significance (Sep 20, 2022)
7-21429601-T-C		not specified	Uncertain significance (Nov 06, 2023)
7-21429602-C-T		not specified	Uncertain significance (Nov 06, 2023)
7-21429608-C-G		not specified	Uncertain significance (Jan 12, 2024)
7-21429610-G-C		not specified	Uncertain significance (May 08, 2023)
7-21429646-G-A		not specified	Uncertain significance (Aug 08, 2022)
7-21429670-C-T		not specified	Uncertain significance (Jun 06, 2023)
7-21429793-G-A		not specified	Uncertain significance (May 02, 2024)
7-21429874-G-A		not specified	Uncertain significance (Jun 29, 2022)
7-21429886-C-G			Benign (Jul 30, 2018)
7-21429896-A-T		not specified	Uncertain significance (Mar 18, 2024)
7-21429910-A-G		not specified	Uncertain significance (Dec 19, 2022)
7-21429925-G-C		not specified	Uncertain significance (Dec 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SP4	protein_coding	protein_coding	ENST00000222584	6	86789

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00712	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.395	386	408	0.945	0.0000200	5058
Missense in Polyphen		85	137.87	0.61653		1754
Synonymous	-0.738	164	152	1.08	0.00000826	1661
Loss of Function	4.62	4	32.4	0.123	0.00000157	336

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000935	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to GT and GC boxes promoters elements. Probable transcriptional activator.

Recessive Scores

• pRec: 0.231

Intolerance Scores

• loftool: 0.378
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.18

Haploinsufficiency Scores

• pHI: 0.903
• hipred: Y
• hipred_score: 0.518
• ghis: 0.616

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.967

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sp4
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); reproductive 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); 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); immune system phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;positive regulation of nucleic acid-templated transcription
• Cellular component: nucleus;nucleoplasm;cytosol
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;transcription coactivator activity;protein binding;sequence-specific DNA binding;metal ion binding