GCSAML
protein-codinggerminal center associated signaling and motility like
Gene summary
This gene encodes a protein thought to be a signaling molecule associated with germinal centers, the sites of proliferation and differentiation of mature B lymphocytes. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
- C1orf150
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~70.6 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 GCSAML variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_145278.5. 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 | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 | 13 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_660321.1 | 5 | MANE Select | |
| Ensembl | ENSP00000355444.4 | 5 | MANE Select | |
| RefSeq | NP_001268763.1 | 4 | Standard | |
| RefSeq | NP_001268764.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of B cell receptor signaling pathway
- regulation of lymphocyte migration
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000366488
- Coding exons
- 5
- Length
- 70633
- Individuals with no LoFs
- 113399
- Homozygous LoFs
- 434
- Heterozygous LoFs
- 11907
- Defined
- 125740
- p
- 0.0503
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.311 | 73 | 65.9 | 1.11 | 0.00000308 | 887 |
| Missense (PolyPhen) | 16 | 16.205 | 0.98733 | 221 | ||
| Synonymous | 1.43 | 15 | 23.9 | 0.628 | 0.00000113 | 235 |
| Loss of Function | 1.37 | 2 | 5.44 | 0.368 | 3.12e-7 | 68 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.034 | 0.033 | notable |
| Latino/Admixed American | 0.031 | 0.030 | notable |
| Ashkenazi Jewish | 0.10 | 0.10 | notable |
| East Asian | 0.025 | 0.024 | notable |
| Finnish | 0.053 | 0.052 | notable |
| European (Non-Finnish) | 0.066 | 0.064 | notable |
| South Asian | 0.030 | 0.029 | notable |
| Other | 0.060 | 0.059 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- RVIS EVS
- 0.33
- RVIS percentile EVS
- 73.11
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |