SPX
protein-codingspexin hormone
Gene summary
The protein encoded by this gene is a hormone involved in modulation of cardiovascular and renal function. It has also been shown in rats to cause weight loss. Several transcript variants have been found for this gene. [provided by RefSeq, Feb 2016]
- C12orf39
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~15.0 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 SPX variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_030572.4. 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 | 18 | 3 | 21 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 21 | 3 | 0 | 24 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_085049.1 | 6 | MANE Select | |
| Ensembl | ENSP00000256969.2 | 6 | MANE Select | |
| Ensembl | ENSP00000497284.1 | 4 | Standard | |
| Ensembl | ENSP00000497284.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- positive regulation of systemic arterial blood pressure
- negative regulation of heart rate
- regulation of signaling receptor activity
- negative regulation of appetite
- negative regulation of renal sodium excretion
Molecular Function
- neuropeptide hormone activity
Cellular Component
- extracellular space
- cytoplasm
- transport vesicle
- dense core granule
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000256969
- Coding exons
- 6
- Length
- 11071
- Individuals with no LoFs
- 125719
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 28
- Defined
- 125747
- p
- 0.000111
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.115 | 63 | 60.5 | 1.04 | 0.00000294 | 737 |
| Missense (PolyPhen) | 17 | 16.839 | 1.0096 | 199 | ||
| Synonymous | 1.74 | 14 | 25.1 | 0.558 | 0.00000136 | 233 |
| Loss of Function | 0.715 | 7 | 9.36 | 0.748 | 6.42e-7 | 84 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000097 | 0.000097 | rare |
| South Asian | 0.00020 | 0.00020 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role as a central modulator of cardiovascular and renal function and nociception. Plays also a role in energy metabolism and storage. Inhibits adrenocortical cell proliferation with minor stimulation on corticosteroid release (By similarity). {ECO:0000250}.; FUNCTION: Spexin-2: Intracerebroventricular administration of the peptide induces a decrease in heart rate, but no change in arterial pressure, and an increase in urine flow rate. Intraventricular administration of the peptide induces antinociceptive activity (By similarity). {ECO:0000250}.;
Intolerance Scores
- RVIS EVS
- 0.06
- RVIS percentile EVS
- 58
Essentials
- Essential (gene trap)
- N