SCX
protein-codingscleraxis bHLH transcription factor, the group of Basic helix-loop-helix proteins
Gene summary
Enables DNA-binding transcription activator activity, RNA polymerase II-specific and bHLH transcription factor binding activity. Contributes to E-box binding activity. Involved in positive regulation of transcription by RNA polymerase II. Located in nucleus. Part of transcription regulator complex. [provided by Alliance of Genome Resources, Jul 2025]
- SCXA
- SCXB
MANE transcript
Inheritance
ClinVar variants
Top phenotype
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~2.0 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 SCX variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001080514.3. 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 | 1 | 1 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 1 | 0 | 0 | 1 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001073983.1 | 2 | MANE Select | |
| Ensembl | ENSP00000476384.1 | 2 | MANE Select | |
| Ensembl | ENSP00000612902.1 | 2 | Standard | |
| Ensembl | ENSP00000612902.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- mesoderm formation
- tissue homeostasis
- endochondral ossification
- chondrocyte differentiation
- heart valve morphogenesis
Molecular Function
- RNA polymerase II distal enhancer sequence-specific DNA binding
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA-binding transcription activator activity, RNA polymerase II-specific
- DNA binding
- bHLH transcription factor binding
Cellular Component
- nucleus
- transcription factor complex
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays an early essential role in mesoderm formation, as well as a later role in formation of somite-derived chondrogenic lineages. {ECO:0000250}.;