SP5
protein-codingSp5 transcription factor, the group of Zinc fingers C2H2-type|Sp transcription factors
Gene summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within bone morphogenesis and post-anal tail morphogenesis. Predicted to be located in chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~2.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SP5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001003845.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 66 | 66 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 66 | 0 | 0 | 66 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001003845.1 | 2 | MANE Select | |
| Ensembl | ENSP00000364430.3 | 2 | MANE Select | |
| Ensembl | ENSP00000810523.1 | 2 | Standard | |
| RefSeq | XP_005246599.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Hair Follicle Development- Induction (Part 1 of 3)
- Regulation of nuclear beta catenin signaling and target gene transcription
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
Molecular Function
- RNA polymerase II regulatory region sequence-specific DNA binding
- DNA-binding transcription factor activity, RNA polymerase II-specific
- metal ion binding
Cellular Component
- nucleus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000375281
- Coding exons
- 2
- Length
- 2728
- Individuals with no LoFs
- 123807
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 4
- Defined
- 123811
- p
- 0.0000162
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0171 | 222 | 221 | 1.00 | 0.0000106 | 2476 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000051 | 0.000047 | rare |
| European (Non-Finnish) | 0.000010 | 0.0000090 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00018 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.116
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.982
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | High | High |