SP5

Sp5 transcription factor, the group of Zinc fingers C2H2-type|Sp transcription factors

Basic information

Region (hg38): 2:170715337-170718078

Links

ENSG00000204335 ∙ NCBI:389058 ∙ OMIM:609391 ∙ HGNC:14529 ∙ Uniprot:Q6BEB4 ∙ 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 SP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SP5 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			35			35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	0	0

Variants in SP5

This is a list of pathogenic ClinVar variants found in the SP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-170716412-C-T		not specified	Uncertain significance (Jan 19, 2025)
2-170716430-G-C		not specified	Uncertain significance (Oct 16, 2024)
2-170716438-G-A		not specified	Uncertain significance (Oct 13, 2023)
2-170716464-C-T		not specified	Uncertain significance (Jun 19, 2024)
2-170716508-C-A		not specified	Uncertain significance (Dec 02, 2024)
2-170716514-C-T		not specified	Uncertain significance (Feb 18, 2025)
2-170716530-C-T		not specified	Uncertain significance (Sep 02, 2024)
2-170716535-G-C		not specified	Uncertain significance (Dec 28, 2022)
2-170716541-C-T		not specified	Uncertain significance (Jun 16, 2023)
2-170716589-G-T		not specified	Uncertain significance (Oct 02, 2023)
2-170716611-T-C		not specified	Uncertain significance (Sep 16, 2021)
2-170716659-C-G		not specified	Uncertain significance (Jan 17, 2024)
2-170716676-C-T		not specified	Uncertain significance (Oct 05, 2023)
2-170716722-C-G		not specified	Uncertain significance (Dec 11, 2023)
2-170716727-A-G		not specified	Uncertain significance (Feb 06, 2023)
2-170716781-A-G		not specified	Uncertain significance (Aug 21, 2023)
2-170716799-G-C		not specified	Uncertain significance (May 04, 2023)
2-170716823-G-C		not specified	Uncertain significance (Aug 02, 2021)
2-170716845-G-T		not specified	Uncertain significance (Jan 26, 2022)
2-170716847-G-A		not specified	Uncertain significance (Nov 18, 2023)
2-170716847-G-C		not specified	Uncertain significance (Jan 24, 2024)
2-170716854-C-A		not specified	Uncertain significance (Aug 17, 2022)
2-170716869-G-C		not specified	Uncertain significance (Sep 24, 2024)
2-170716889-G-A		not specified	Uncertain significance (Dec 11, 2023)
2-170716895-G-A		not specified	Uncertain significance (Mar 03, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SP5	protein_coding	protein_coding	ENST00000375281	2	2728

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.518	0.478	123807	0	4	123811	0.0000162

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0171	222	221	1.00	0.0000106	2476
Missense in Polyphen		18	14.806	1.2157		151
Synonymous	-1.41	128	109	1.17	0.00000558	887
Loss of Function	2.45	2	10.6	0.189	4.56e-7	111

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	0.0000513	0.0000471
European (Non-Finnish)	0.0000101	0.00000898
Middle Eastern	0.00	0.00
South Asian	0.0000335	0.0000327
Other	0.000176	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to GC boxes promoters elements. Probable transcriptional activator that has a role in the coordination of changes in transcription required to generate pattern in the developing embryo (By similarity). {ECO:0000250}.
• Pathway: Hair Follicle Development- Induction (Part 1 of 3);Regulation of nuclear beta catenin signaling and target gene transcription (Consensus)

Recessive Scores

• pRec: 0.116

Haploinsufficiency Scores

• pHI: 0.592
• hipred: Y
• hipred_score: 0.747
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.982

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sp5
• Phenotype: skeleton phenotype; hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; normal phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;post-anal tail morphogenesis;bone morphogenesis;cellular response to organic cyclic compound
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;metal ion binding