ALKAL1

ALK and LTK ligand 1

Basic information

Region (hg38): 8:52534037-52565430

Previous symbols: [ "FAM150A" ]

Links

ENSG00000196711 ∙ NCBI:389658 ∙ OMIM:619670 ∙ HGNC:33775 ∙ Uniprot:Q6UXT8 ∙ 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 ALKAL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALKAL1 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in ALKAL1

This is a list of pathogenic ClinVar variants found in the ALKAL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-52539869-C-A		not specified	Uncertain significance (Jan 23, 2024)
8-52539877-A-C		not specified	Uncertain significance (May 26, 2024)
8-52539893-G-T		not specified	Uncertain significance (Feb 10, 2023)
8-52565078-G-A		not specified	Uncertain significance (Jan 03, 2024)
8-52565087-G-C		not specified	Uncertain significance (May 18, 2022)
8-52565097-C-T		not specified	Uncertain significance (Apr 23, 2024)
8-52565105-G-A		not specified	Uncertain significance (Jan 24, 2024)
8-52565121-G-C		not specified	Uncertain significance (Dec 12, 2022)
8-52565160-T-A		not specified	Uncertain significance (Jun 13, 2024)
8-52565207-G-A		not specified	Uncertain significance (Mar 01, 2024)
8-52565220-G-C		not specified	Uncertain significance (Dec 16, 2022)
8-52565226-G-A		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALKAL1	protein_coding	protein_coding	ENST00000358543	4	31471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000591	0.283	125713	0	22	125735	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.516	39	49.2	0.793	0.00000248	798
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000150	0.000150
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000545	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.000334	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• 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}.

Haploinsufficiency Scores

• pHI: 0.216
• hipred: N
• hipred_score: 0.243
• ghis: 0.459

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Alkal1

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