ALKAL2

protein-coding

ALK and LTK ligand 2

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 neuroblastoma. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

FAM150B

MANE transcript

NM_001002919.3

Inheritance

—

ClinVar variants

U:36B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.49

Max pathogenic AF

—

Genomic locus

chr2:279,558-288,851

External References & Databases

Ensembl (ENSG00000189292)

Transcript & Mutation Effects

hg38 • Region Span ~9.3 kb

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GenCC 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 ALKAL2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 34

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001002919.3. 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 clinvar	1 clinvar		2
missense			33 clinvar	1 clinvar		34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	36	2	0	38

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001002919.3	RefSeq	NP_001002919.2	5	MANE Select
ENST00000403610.9	Ensembl	ENSP00000384604.3	5	MANE Select
ENST00000344414.10	Ensembl	ENSP00000339565.5	4	Standard
ENST00000344414.9	Ensembl	ENSP00000339565.5	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: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000403610
Coding exons: 5
Length: 9294
Individuals with no LoFs: 124620
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 124623
p: 0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.701	64	50.0	1.28	0.00000245	932
Missense (PolyPhen)		14	27.667	0.50603		381
Synonymous	-2.96	35	18.7	1.87	9.49e-7	324
Loss of Function	1.15	3	6.07	0.495	3.22e-7	85

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Ligand for receptor tyrosine kinases LTK and ALK. Stimulation of ALK signaling may be involved in regulation of cell proliferation and transformation. {ECO:0000269|PubMed:26418745, ECO:0000269|PubMed:26630010}.;

Essentials

Essential (gene trap): N