ALKAL2

ALK and LTK ligand 2

Basic information

Region (hg38): 2:279558-288851

Previous symbols: [ "FAM150B" ]

Links

ENSG00000189292 ∙ NCBI:285016 ∙ OMIM:619671 ∙ HGNC:27683 ∙ Uniprot:Q6UX46 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ALKAL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALKAL2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in ALKAL2

This is a list of pathogenic ClinVar variants found in the ALKAL2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-283118-T-G		not specified	Uncertain significance (Apr 04, 2024)
2-286153-G-A		not specified	Uncertain significance (May 24, 2023)
2-286296-G-T		not specified	Uncertain significance (Sep 14, 2021)
2-286312-G-C		not specified	Uncertain significance (Dec 18, 2023)
2-287612-C-G		not specified	Uncertain significance (Apr 20, 2023)
2-287652-G-A		not specified	Uncertain significance (Apr 09, 2024)
2-287670-G-A		not specified	Uncertain significance (Feb 06, 2023)
2-287721-G-A		not specified	Uncertain significance (May 09, 2024)
2-287732-T-C		not specified	Uncertain significance (Dec 07, 2021)
2-287736-C-T		not specified	Likely benign (Sep 09, 2021)
2-287744-G-C		not specified	Uncertain significance (Jun 17, 2024)
2-287760-C-G		not specified	Uncertain significance (Sep 29, 2023)
2-287768-C-G		not specified	Uncertain significance (Sep 27, 2022)
2-287784-C-T		not specified	Uncertain significance (Mar 17, 2023)
2-287811-G-A		not specified	Uncertain significance (Feb 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALKAL2	protein_coding	protein_coding	ENST00000403610	5	9294

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0318	0.827	124620	0	3	124623	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.701	64	50.0	1.28	0.00000245	932
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000111	0.000111
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.

Haploinsufficiency Scores

• pHI: 0.00641
• hipred: N
• hipred_score: 0.396
• ghis: 0.444

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Alkal2

Gene ontology

• 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
• Cellular component: extracellular region
• Molecular function: protein binding;receptor signaling protein tyrosine kinase activator activity;receptor tyrosine kinase binding