ALPI

alkaline phosphatase, intestinal, the group of Alkaline phosphatases

Basic information

Region (hg38): 2:232456125-232460753

Links

ENSG00000163295 ∙ NCBI:248 ∙ OMIM:171740 ∙ HGNC:437 ∙ Uniprot:P09923 ∙ 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 ALPI gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALPI 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			47	2		49
nonsense		1	1			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	1	48	2	2

Variants in ALPI

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

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

Position	Type	Phenotype	Significance	ClinVar
2-232456193-C-G		ALPI-related disorder	Likely benign (Oct 28, 2019)
2-232456219-T-C		not specified • ALPI-related disorder	Uncertain significance (Jan 09, 2024)
2-232456225-T-C			Uncertain significance (May 09, 2024)
2-232456257-G-A		ALPI-related disorder	Benign (Apr 04, 2019)
2-232456364-C-T		Inflammatory bowel disease	Uncertain significance (Dec 05, 2023)
2-232456379-G-T		ALPI-related disorder	Benign (May 23, 2019)
2-232456414-C-A		not specified	Uncertain significance (May 23, 2023)
2-232456434-C-T		ALPI-related disorder	Likely benign (Aug 06, 2024)
2-232456595-C-T		not specified	Uncertain significance (Sep 19, 2022)
2-232456669-C-T		ALPI-related disorder	Uncertain significance (Aug 16, 2023)
2-232456675-C-T		not specified	Uncertain significance (Jun 10, 2024)
2-232456685-C-G		not specified	Uncertain significance (Sep 27, 2022)
2-232456691-C-A		not specified	Uncertain significance (Jan 03, 2022)
2-232456931-C-T		ALPI-related disorder	Benign (Nov 20, 2019)
2-232456959-G-A		not specified	Uncertain significance (Oct 06, 2022)
2-232456969-C-G		not specified	Uncertain significance (Jul 22, 2024)
2-232456969-C-T		not specified	Uncertain significance (Jul 06, 2021)
2-232456986-G-A		not specified	Uncertain significance (Feb 10, 2025)
2-232456994-T-G		not specified	Uncertain significance (Mar 28, 2024)
2-232457004-C-T		Inflammatory bowel disease	Uncertain significance (Dec 05, 2023)
2-232457014-A-C		not specified	Uncertain significance (Mar 19, 2024)
2-232457023-C-T		not specified	Uncertain significance (Oct 06, 2021)
2-232457029-G-A		ALPI-related disorder	Benign (May 23, 2019)
2-232457036-T-A		ALPI-related disorder	Benign (Sep 25, 2019)
2-232457059-G-A			Uncertain significance (Mar 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALPI	protein_coding	protein_coding	ENST00000295463	11	3910

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.45e-18	0.00209	125505	0	239	125744	0.000951

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.403	327	348	0.939	0.0000227	3375
Missense in Polyphen		95	113.93	0.83383		1062
Synonymous	0.519	156	164	0.949	0.0000124	1097
Loss of Function	-0.326	26	24.3	1.07	0.00000131	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000990	0.000988
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.00104	0.00103
Finnish	0.00	0.00
European (Non-Finnish)	0.000336	0.000334
Middle Eastern	0.00104	0.00103
South Asian	0.00508	0.00508
Other	0.000336	0.000326

dbNSFP

Source: dbNSFP

• Pathway: Folate biosynthesis - Homo sapiens (human);Thiamine metabolism - Homo sapiens (human);Vitamin D Receptor Pathway;Metabolism of lipids;Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins;Metabolism;pyridoxal 5,-phosphate salvage;Glycerophospholipid biosynthesis;Phospholipid metabolism;Digestion;Digestion and absorption;Synthesis of PA (Consensus)

Recessive Scores

• pRec: 0.910

Intolerance Scores

• loftool: 0.248
• rvis_EVS: -0.39
• rvis_percentile_EVS: 27.03

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.139
• ghis: 0.452

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Alppl2
• Phenotype: growth/size/body region phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; embryo phenotype

Zebrafish Information Network

• Gene name: alpi.1
• Affected structure: alkaline phosphatase activity
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: phosphatidic acid biosynthetic process;digestion;dephosphorylation
• Cellular component: extracellular region;plasma membrane;anchored component of membrane
• Molecular function: magnesium ion binding;protease binding;alkaline phosphatase activity;protein binding;zinc ion binding