ALKAL1
protein-codingALK and LTK ligand 1
Gene summary
Enables cytokine activity; receptor signaling protein tyrosine kinase activator activity; and receptor tyrosine kinase binding activity. Involved in cell surface receptor protein tyrosine kinase signaling pathway; positive regulation of MAPK cascade; and positive regulation of neuron projection development. Is active in obsolete extracellular space. Implicated in cancer and neuroblastoma. [provided by Alliance of Genome Resources, Jun 2026]
- FAM150A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~31.4 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 ALKAL1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_207413.4. 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 | 24 | 1 | 25 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 24 | 1 | 0 | 25 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_997296.1 | 4 | MANE Select | |
| Ensembl | ENSP00000351345.4 | 4 | MANE Select | |
| Ensembl | ENSP00000430953.1 | 4 | Standard | |
| Ensembl | ENSP00000430953.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- positive regulation of neuron projection development
- positive regulation of protein tyrosine kinase activity
- positive regulation of ERK1 and ERK2 cascade
- positive regulation of ERK5 cascade
Molecular Function
- protein binding
- receptor signaling protein tyrosine kinase activator activity
- receptor tyrosine kinase binding
Cellular Component
- extracellular region
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000358543
- Coding exons
- 4
- Length
- 31471
- Individuals with no LoFs
- 125713
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 22
- Defined
- 125735
- p
- 0.0000875
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.516 | 39 | 49.2 | 0.793 | 0.00000248 | 798 |
| Missense (PolyPhen) | 20 | 21.648 | 0.92389 | 296 | ||
| Synonymous | 0.788 | 16 | 20.5 | 0.779 | 0.00000114 | 269 |
| Loss of Function | -0.263 | 6 | 5.34 | 1.12 | 3.09e-7 | 82 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000055 | 0.000053 | rare |
| South Asian | 0.00033 | 0.00029 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Ligand for receptor tyrosine kinase LTK and perhaps receptor tyrosine kinase ALK; activation of ALK is reported conflictingly. {ECO:0000269|PubMed:25331893, ECO:0000269|PubMed:26418745, ECO:0000269|PubMed:26630010}.;
Essentials
- Essential (gene trap)
- N