ALPP

alkaline phosphatase, placental, the group of Alkaline phosphatases

Basic information

Region (hg38): 2:232378723-232382889

Links

ENSG00000163283 ∙ NCBI:250 ∙ OMIM:171800 ∙ HGNC:439 ∙ Uniprot:P05187 ∙ 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 ALPP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALPP 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				3	3	6
missense			49	2	3	54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding				1		1
Total	0	0	49	6	6

Variants in ALPP

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

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

Position	Type	Phenotype	Significance	ClinVar
2-232378840-T-C		not specified	Uncertain significance (Jun 23, 2023)
2-232378856-G-T		not specified	Uncertain significance (Apr 17, 2024)
2-232378876-C-T		ALKALINE PHOSPHATASE, PLACENTAL, ALLELE-3 POLYMORPHISM	Benign (Aug 01, 1986)
2-232378876-C-C		ALKALINE PHOSPHATASE, PLACENTAL, ALLELE-1 POLYMORPHISM	Benign (Aug 01, 1986)
2-232378962-C-T			Likely benign (May 31, 2018)
2-232379001-G-A		not specified	Uncertain significance (Sep 17, 2021)
2-232379002-C-T			Benign (May 30, 2017)
2-232379003-G-C			Benign (Sep 03, 2018)
2-232379027-G-A		not specified	Uncertain significance (Oct 26, 2022)
2-232379082-G-T		not specified	Uncertain significance (Jan 23, 2023)
2-232379083-C-G			Likely benign (Mar 28, 2018)
2-232379215-C-T		not specified	Uncertain significance (Nov 08, 2022)
2-232379265-C-A		not specified	Uncertain significance (Jan 23, 2023)
2-232379275-C-G		not specified	Uncertain significance (Oct 05, 2023)
2-232379567-C-G		not specified	Uncertain significance (Sep 26, 2023)
2-232379579-A-C		not specified	Uncertain significance (Dec 02, 2021)
2-232379618-C-T		not specified	Uncertain significance (Dec 19, 2023)
2-232379619-G-A		not specified	Uncertain significance (May 14, 2024)
2-232379630-T-C		not specified	Uncertain significance (Jun 16, 2024)
2-232379645-G-C		not specified	Uncertain significance (Feb 15, 2023)
2-232379658-T-A		not specified	Uncertain significance (Dec 06, 2021)
2-232379797-T-A		not specified	Uncertain significance (Mar 13, 2023)
2-232379805-G-T		not specified	Uncertain significance (Jan 22, 2024)
2-232379806-C-G		not specified	Uncertain significance (Jan 22, 2024)
2-232379807-C-A			Benign (Aug 16, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALPP	protein_coding	protein_coding	ENST00000392027	11	4356

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.81e-13	0.0571	125656	0	90	125746	0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.448	364	341	1.07	0.0000229	3364
Missense in Polyphen		148	135.89	1.0891		1398
Synonymous	1.26	137	157	0.872	0.0000120	1117
Loss of Function	0.452	21	23.4	0.899	0.00000141	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00143	0.00142
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00103	0.00103
Finnish	0.00	0.00
European (Non-Finnish)	0.000231	0.000229
Middle Eastern	0.00103	0.00103
South Asian	0.000264	0.000261
Other	0.000991	0.000978

dbNSFP

Source: dbNSFP

• Pathway: Folate biosynthesis - Homo sapiens (human);Thiamine metabolism - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Intra-Golgi traffic;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.137

Intolerance Scores

• loftool: 0.174
• rvis_EVS: 1.36
• rvis_percentile_EVS: 94.44

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Gene ontology

• Biological process: dephosphorylation
• Cellular component: plasma membrane;cell surface;integral component of membrane;anchored component of membrane
• Molecular function: magnesium ion binding;alkaline phosphatase activity;protein binding;zinc ion binding