ALPG

alkaline phosphatase, germ cell, the group of Alkaline phosphatases

Basic information

Region (hg38): 2:232406844-232410714

Previous symbols: [ "ALPPL2" ]

Links

ENSG00000163286 ∙ NCBI:251 ∙ OMIM:171810 ∙ HGNC:441 ∙ Uniprot:P10696 ∙ 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 ALPG gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALPG 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	5	8
missense			45	3	4	52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	45	7	9

Variants in ALPG

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

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

Position	Type	Phenotype	Significance	ClinVar
2-232406916-C-T		not specified	Uncertain significance (Jul 08, 2022)
2-232406918-C-T			Benign (Dec 04, 2017)
2-232407086-C-T		not specified	Uncertain significance (Mar 04, 2024)
2-232407087-G-A		not specified	Uncertain significance (Jan 04, 2022)
2-232407097-C-T			Likely benign (Jul 01, 2022)
2-232407099-A-C		not specified	Uncertain significance (Jun 10, 2022)
2-232407113-G-A		not specified	Uncertain significance (Jan 30, 2024)
2-232407138-C-G		not specified	Uncertain significance (Oct 17, 2023)
2-232407142-C-T			Benign (Dec 31, 2019)
2-232407143-G-A		not specified	Uncertain significance (Mar 14, 2023)
2-232407158-A-G		not specified	Uncertain significance (Oct 10, 2023)
2-232407291-G-C		not specified	Uncertain significance (Apr 30, 2024)
2-232407381-C-T			Benign (Feb 25, 2018)
2-232407385-A-T			Benign (Nov 08, 2017)
2-232407595-C-T		not specified	Uncertain significance (May 06, 2024)
2-232407653-C-G		not specified	Uncertain significance (Feb 13, 2024)
2-232407654-G-A		not specified	Uncertain significance (Jan 13, 2023)
2-232407696-G-A		not specified	Uncertain significance (Dec 05, 2022)
2-232407699-C-T		not specified	Uncertain significance (Dec 22, 2023)
2-232407700-G-T		not specified	Uncertain significance (Dec 28, 2022)
2-232407732-G-A		not specified	Uncertain significance (Mar 26, 2024)
2-232407743-C-T			Benign (Dec 04, 2017)
2-232407744-G-A		not specified	Uncertain significance (Mar 22, 2022)
2-232407849-G-C		not specified	Uncertain significance (May 31, 2023)
2-232407874-C-T		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALPG	protein_coding	protein_coding	ENST00000295453	11	3872

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.49e-11	0.105	125656	2	73	125731	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0160	326	327	0.998	0.0000230	3371
Missense in Polyphen		103	104.8	0.98283		1106
Synonymous	-1.02	168	152	1.11	0.0000124	1117
Loss of Function	0.471	18	20.3	0.887	9.78e-7	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.000850
Ashkenazi Jewish	0.00109	0.00109
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000222	0.000220
Middle Eastern	0.000163	0.000163
South Asian	0.000431	0.000425
Other	0.000817	0.000815

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.187

Intolerance Scores

• rvis_EVS: 0.47
• rvis_percentile_EVS: 78.8

Haploinsufficiency Scores

• pHI: 0.0659
• hipred: N
• hipred_score: 0.187
• ghis: 0.413

Essentials

• essential_gene_gene_trap: N

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

Gene ontology

• Biological process: dephosphorylation
• Cellular component: extracellular region;plasma membrane;anchored component of membrane
• Molecular function: alkaline phosphatase activity;metal ion binding