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Primary immunodeficiency

Gene: ALPI

Green List (high evidence)

ALPI (alkaline phosphatase, intestinal)
EnsemblGeneIds (GRCh38): ENSG00000163295
EnsemblGeneIds (GRCh37): ENSG00000163295
OMIM: 171740, Gene2Phenotype
ALPI is in 2 panels

4 reviews

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

This gene has been confirmed for this panel by the NHS Genomic Medicine Service as the eligibility criteria of R15 has been extended to include IBD genes and should be rated green.
Created: 8 Mar 2022, 3:09 p.m. | Last Modified: 8 Mar 2022, 3:09 p.m.
Panel Version: 2.536

Eleanor Williams (Genomics England Curator)

Comment on list classification: Changing rating from red to amber. 2 cases reported plus some functional data.
Created: 23 Apr 2020, 2:11 a.m. | Last Modified: 23 Apr 2020, 2:11 a.m.
Panel Version: 2.128
Not associated with a phenotype in OMIM or Gene2Phenotype.

PMID: 29567797 - Parlato et al 2018- report ALPI mutations in two unrelated patients with severe intestinal inflammation and autoimmunity. WES was used. Patient 1 - non‐consanguineous parents. At 2 years old was diagnosed with coeliac disease from HLA-typing. At age 3 had recurrent abdominal pain, rectal bleeding and severe diarrhoea. Patient 2 - non‐consanguineous parents of Jewish Ashkenazi origin. Age 15 he was diagnosed with ileocolonic Crohn's disease. Compound heterozygous mutations in the ALPI gene were found in both patients. Three variants result in the substitution of residues highly conserved across species (A97T, A350V and A360) and one variant (Q439X) introducing a premature stop codon. Functional studies in HEK293T cells showed that all ALPI mutations were loss of function. ALPI expression was reduced in patients’ biopsies.
Created: 23 Apr 2020, 2:08 a.m. | Last Modified: 23 Apr 2020, 2:09 a.m.
Panel Version: 2.127

Zornitza Stark (Australian Genomics)

I don't know

Two unrelated individuals, some functional data.
Created: 9 Apr 2020, 12:39 a.m. | Last Modified: 9 Apr 2020, 12:39 a.m.
Panel Version: 2.46

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Inflammatory bowel disease

Publications

Louise Daugherty (Genomics England Curator)

I don't know

Added publication referenced by IUIS december 2019 update
Created: 28 Feb 2020, 8:49 p.m. | Last Modified: 28 Feb 2020, 8:49 p.m.
Panel Version: 2.36

Publications

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • IUIS Classification December 2019
Phenotypes
  • Intestinal Alkaline Phosphatase deficiency
  • Inflammatory bowel disease
  • Autoinflammatory Disorders
  • ALPI deficiency
Tags
gene-checked
OMIM
171740
Clinvar variants
Variants in ALPI
Penetrance
None
Publications
Panels with this gene

History Filter Activity

4 May 2022, Gel status: 3

Added Tag

Catherine Snow (Genomics England)

Tag gene-checked tag was added to gene: ALPI.

8 Mar 2022, Gel status: 3

Added New Source, Set Phenotypes, Set publications, Status Update

Arina Puzriakova (Genomics England Curator)

Source Expert Review Green was added to ALPI. Added phenotypes Intestinal Alkaline Phosphatase deficiency for gene: ALPI Publications for gene: ALPI were updated from 32086639; 32048120; 29567797 to 32048120; 29567797; 32086639 Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

23 Apr 2020, Gel status: 2

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: alpi has been classified as Amber List (Moderate Evidence).

28 Feb 2020, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene ALPI were updated from 32086639; 32048120 to 32086639; 32048120; 29567797

26 Feb 2020, Gel status: 1

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Louise Daugherty (Genomics England Curator)

gene: ALPI was added gene: ALPI was added to Primary immunodeficiency. Sources: IUIS Classification December 2019 Mode of inheritance for gene: ALPI was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ALPI were set to 32086639; 32048120 Phenotypes for gene: ALPI were set to Autoinflammatory Disorders; ALPI deficiency; Inflammatory bowel disease