ALPG

protein-coding

alkaline phosphatase, germ cell, the group of Alkaline phosphatases

Gene summary

There are at least four distinct but related alkaline phosphatases: intestinal, placental, placental-like, and liver/bone/kidney (tissue non-specific). The product of this gene is a membrane bound glycosylated enzyme, localized to testis, thymus and certain germ cell tumors, that is closely related to both the placental and intestinal forms of alkaline phosphatase. [provided by RefSeq, Jul 2008]

Previous symbols:

ALPPL2

MANE transcript

NM_031313.3

Inheritance

—

ClinVar variants

U:107B:20

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.89

Max pathogenic AF

—

Genomic locus

chr2:232,406,844-232,410,714

External References & Databases

Ensembl (ENSG00000163286)

Transcript & Mutation Effects

hg38 • Region Span ~3.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ALPG variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 114

not providedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031313.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar	4 clinvar	8
missense			106 clinvar	10 clinvar	2 clinvar	118
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	107	14	6	127

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031313.3	RefSeq	NP_112603.2	11	MANE Select
ENST00000295453.8	Ensembl	ENSP00000295453.3	11	MANE Select
ENST00001144046.1	Ensembl	ENSP00000805011.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

dephosphorylation

Molecular Function

alkaline phosphatase activity
metal ion binding

Cellular Component

extracellular region
plasma membrane
anchored component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000295453
Coding exons: 11
Length: 3872
Individuals with no LoFs: 125656
Homozygous LoFs: 2
Heterozygous LoFs: 73
Defined: 125731
p: 0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0160	326	327	0.998	0.0000230	3371
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00084	0.00068	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0.0011	0.0011	notable
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00022	0.00022	rare
South Asian	0.00043	0.00042	rare
Other	0.00082	0.00082	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.187

Intolerance Scores

RVIS EVS: 0.47
RVIS percentile EVS: 78.8

Essentials

Essential (gene trap): N