ALPP

alkaline phosphatase, placental, the group of Alkaline phosphatases

Basic information

Region (hg38): 2:232378724-232382889

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.

• not_specified (108 variants)
• not_provided (9 variants)

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. These statistics are base on transcript: NM_000001632.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	4	5
missense			104	5	2	111
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	104	6	6

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