CSHL1
protein-codingchorionic somatomammotropin hormone like 1, the group of Growth hormone family
Gene summary
The protein encoded by this gene is a member of the somatotropin/prolactin family of hormones which play an important role in growth control. The gene, along with four other related genes, is located at the growth hormone locus on chromosome 17 where they are interspersed in the same transcriptional orientation; an arrangement which is thought to have evolved by a series of gene duplications. Although the five genes share a remarkably high degree of sequence identity, they are expressed selectively in different tissues. This particular family member is expressed in placental villi, although it was originally thought to be a pseudogene. In fact, alternative splicing suggests that the majority of the transcripts would be unable to express a secreted protein. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
- CSHP1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~1.7 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 CSHL1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022579.3. 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 | 1 | 1 | ||||
| missense | 49 | 8 | 2 | 59 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 49 | 9 | 3 | 61 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_072101.1 | 5 | MANE Select | |
| Ensembl | ENSP00000309524.5 | 5 | MANE Select | |
| RefSeq | NP_001309.3 | 3 | Standard | |
| RefSeq | NP_001307996.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- biological_process
- regulation of signaling receptor activity
- response to nutrient levels
- positive regulation of tyrosine phosphorylation of STAT protein
- positive regulation of growth
Molecular Function
- growth hormone receptor binding
- hormone activity
- growth factor activity
- metal ion binding
Cellular Component
- cellular_component
- extracellular space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000309894
- Coding exons
- 5
- Length
- 9242
- Individuals with no LoFs
- 124741
- Homozygous LoFs
- 21
- Heterozygous LoFs
- 986
- Defined
- 125748
- p
- 0.00401
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.74 | 181 | 126 | 1.43 | 0.00000798 | 1454 |
| Missense (PolyPhen) | 85 | 60.539 | 1.404 | 772 | ||
| Synonymous | -2.53 | 79 | 55.1 | 1.43 | 0.00000359 | 427 |
| Loss of Function | -1.30 | 15 | 10.5 | 1.43 | 5.56e-7 | 113 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.045 | 0.045 | notable |
| Latino/Admixed American | 0.0025 | 0.0025 | notable |
| Ashkenazi Jewish | 0.0025 | 0.0025 | notable |
| East Asian | 0.0033 | 0.0033 | notable |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00069 | 0.00068 | rare |
| South Asian | 0.00056 | 0.00056 | rare |
| Other | 0.0037 | 0.0038 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be a novel gestational hormone required to compensate for absence of other members of the GH/CS cluster during gestation. {ECO:0000269|PubMed:8083227}.;
Recessive Scores
- pRec
- 0.0881
Intolerance Scores
- LoFtool
- 0.123
- RVIS EVS
- 1.2
- RVIS percentile EVS
- 92.95
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.506
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |