Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	249
Gene name Gene Name - the full gene name approved by the HGNC.	Alkaline phosphatase, biomineralization associated
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	ALPL
Synonyms (NCBI Gene) Gene synonyms aliases	AP-TNAP, APTNAP, HOPS, HPPA, HPPC, HPPI, HPPO, TNALP, TNAP, TNS-ALP, TNSALP
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1p36.12
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a member of the alkaline phosphatase family of proteins. There are at least four distinct but related alkaline phosphatases: intestinal, placental, placental-like, and liver/bone/kidney (tissue non-specific). The first three are located

Show/Hide all(95)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121918000	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs121918001	C>A,T	Likely-pathogenic	Missense variant, intron variant, coding sequence variant
rs121918002	A>C	Pathogenic	Missense variant, coding sequence variant
rs121918003	G>A,C	Pathogenic	Missense variant, intron variant, coding sequence variant
rs121918004	A>C	Pathogenic	Missense variant, coding sequence variant
rs121918005	C>G,T	Pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant, upstream transcript variant, genic upstream transcript variant
rs121918006	T>C	Pathogenic	Missense variant, coding sequence variant
rs121918007	G>A,C	Pathogenic-likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs121918008	A>T	Pathogenic	Missense variant, coding sequence variant
rs121918009	G>A	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs121918010	T>C	Pathogenic-likely-pathogenic, pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs121918011	G>A,C	Pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs121918012	G>T	Pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs121918013	G>A	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs121918014	A>G	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs121918015	C>T	Pathogenic	Missense variant, coding sequence variant
rs121918016	G>A	Pathogenic	Missense variant, coding sequence variant
rs121918017	G>A,C	Pathogenic	Missense variant, coding sequence variant
rs121918018	G>C,T	Pathogenic-likely-pathogenic, pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs121918019	G>A,C	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs121918020	C>T	Pathogenic	Missense variant, coding sequence variant
rs139811782	G>A	Likely-pathogenic	Missense variant, intron variant, coding sequence variant
rs141448778	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs148405563	C>G,T	Conflicting-interpretations-of-pathogenicity, likely-benign	Missense variant, coding sequence variant
rs149889416	G>A	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs199590449	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs199665722	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs199669988	G>A	Pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs370122334	C>A,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs371243939	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs376221105	C>A,G,T	Pathogenic	Coding sequence variant, missense variant, stop gained
rs387906525	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs749544042	G>A	Pathogenic	Splice donor variant
rs750174638	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs751404811	C>-,CC	Likely-pathogenic	Frameshift variant, coding sequence variant
rs751994699	GG>-	Pathogenic	Frameshift variant, coding sequence variant
rs753338851	CTT>-	Pathogenic, likely-pathogenic	Coding sequence variant, inframe deletion
rs754826836	->T	Likely-pathogenic	Frameshift variant, coding sequence variant
rs755529290	C>A,T	Likely-pathogenic	Synonymous variant, coding sequence variant, stop gained
rs760134827	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs763159520	C>T	Likely-pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs763244290	T>-	Likely-pathogenic	Frameshift variant, 5 prime UTR variant, coding sequence variant
rs764322898	T>G	Likely-pathogenic	Intron variant, splice donor variant, genic upstream transcript variant
rs764908423	->G	Likely-pathogenic	Frameshift variant, coding sequence variant
rs766076920	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs768160006	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs769948289	G>-,GG	Likely-pathogenic	Coding sequence variant, frameshift variant
rs771540767	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs772638759	ACCCCCTGAGCGTCCT>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs773257111	G>A	Pathogenic	Missense variant, coding sequence variant
rs781264043	T>C	Likely-pathogenic	Missense variant, coding sequence variant, intron variant
rs781272386	G>A,C,T	Likely-pathogenic	Missense variant, coding sequence variant
rs786204442	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs786204473	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs786204530	AC>CA	Pathogenic, not-provided, likely-pathogenic	Missense variant, coding sequence variant
rs786204634	G>A	Likely-pathogenic	Coding sequence variant, stop gained
rs886044912	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1057516230	AACT>-	Likely-pathogenic, pathogenic	Frameshift variant, intron variant, coding sequence variant, genic upstream transcript variant
rs1057516293	C>T	Likely-pathogenic	Stop gained, 5 prime UTR variant, coding sequence variant, synonymous variant
rs1057516334	C>T	Likely-pathogenic	5 prime UTR variant, coding sequence variant, genic upstream transcript variant, upstream transcript variant, stop gained
rs1057516526	C>-,CC	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1057516622	A>G	Likely-pathogenic	Splice acceptor variant
rs1057516702	TC>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1057517173	G>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1057517304	T>A	Likely-pathogenic	Splice donor variant, intron variant
rs1057517321	A>-	Likely-pathogenic	Frameshift variant, 5 prime UTR variant, coding sequence variant, genic upstream transcript variant, upstream transcript variant
rs1057517322	->GCAG	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1057517337	CCTGCTGCTCGCGCTGGCCC>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1057517391	T>A,G	Pathogenic	Splice donor variant
rs1131691372	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs1201942473	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs1344601362	CT>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1413274209	G>A	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs1553411779	G>A	Likely-pathogenic	Coding sequence variant, stop gained, genic upstream transcript variant, 5 prime UTR variant, upstream transcript variant
rs1553411890	->G	Likely-pathogenic	Splice acceptor variant, coding sequence variant, intron variant
rs1553411896	GCTGCCCG>-	Likely-pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1553411920	->TCAG	Likely-pathogenic	Intron variant, coding sequence variant, frameshift variant
rs1553412246	C>-	Likely-pathogenic	Stop gained, coding sequence variant
rs1553412310	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1553413512	G>A	Likely-pathogenic	Splice donor variant
rs1553414078	AGGGGAC>T	Likely-pathogenic	Inframe deletion, coding sequence variant
rs1553414111	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs1553414133	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1553414560	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1553414600	CT>-	Likely-pathogenic, pathogenic	Coding sequence variant, frameshift variant
rs1553414843	GACA>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1553415035	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1553415164	CT>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1558543066	A>-	Pathogenic	Intron variant, frameshift variant, coding sequence variant, genic upstream transcript variant
rs1558548925	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1558557341	CTC>-	Pathogenic	Inframe deletion, coding sequence variant
rs1558557428	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1558558939	T>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1558558976	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1570276921	G>A	Likely-pathogenic	Coding sequence variant, missense variant

Show/Hide all(9)

miRTarBase ID	miRNA	Experiments	Reference
MIRT007116	hsa-miR-204-5p	Luciferase reporter assay	23472141
MIRT007116	hsa-miR-204-5p	Luciferase reporter assay	23472141
MIRT007116	hsa-miR-204-5p	Luciferase reporter assay, Western blotting, Immunofluorescence, qRT-PCR, In situ hybridization, Flow cytometry	33138854
MIRT735033	hsa-miR-149-3p	Luciferase reporter assay, Western blotting, Microarray	32898999
MIRT755689	hsa-miR-26a-5p	Western blotting, qRT-PCR, Flow cytometry	35246197
MIRT779124	hsa-miR-4433	CLIP-seq
MIRT779125	hsa-miR-665	CLIP-seq
MIRT1930002	hsa-miR-3127-3p	CLIP-seq
MIRT2170742	hsa-miR-122	CLIP-seq

Transcription factors

Show/Hide all(1)

Transcription factor	Regulation	Reference
SP3	Activation	11073119

Show/Hide all(64)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001501	Process	Skeletal system development	TAS	9781036
GO:0001649	Process	Osteoblast differentiation	HDA	16210410
GO:0001958	Process	Endochondral ossification	IEA
GO:0003006	Process	Developmental process involved in reproduction	IEA
GO:0004035	Function	Alkaline phosphatase activity	IBA
GO:0004035	Function	Alkaline phosphatase activity	IDA	12162492, 33821301
GO:0004035	Function	Alkaline phosphatase activity	IEA
GO:0004427	Function	Inorganic diphosphate phosphatase activity	IEA
GO:0005509	Function	Calcium ion binding	IDA	11395499
GO:0005576	Component	Extracellular region	TAS
GO:0005615	Component	Extracellular space	IEA
GO:0005739	Component	Mitochondrion	IEA
GO:0005758	Component	Mitochondrial intermembrane space	IEA
GO:0005758	Component	Mitochondrial intermembrane space	IEA
GO:0005758	Component	Mitochondrial intermembrane space	ISS
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA	2220817, 33821301
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0016020	Component	Membrane	HDA	16210410
GO:0016020	Component	Membrane	IEA
GO:0016462	Function	Pyrophosphatase activity	IDA	12162492, 19874193
GO:0016462	Function	Pyrophosphatase activity	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016791	Function	Phosphatase activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0019725	Process	Cellular homeostasis	IEA
GO:0030282	Process	Bone mineralization	IBA
GO:0030282	Process	Bone mineralization	IEA
GO:0030282	Process	Bone mineralization	ISS
GO:0031012	Component	Extracellular matrix	IEA
GO:0031214	Process	Biomineral tissue development	IEA
GO:0031966	Component	Mitochondrial membrane	IEA
GO:0031966	Component	Mitochondrial membrane	IEA
GO:0031966	Component	Mitochondrial membrane	ISS
GO:0032496	Process	Response to lipopolysaccharide	IEA
GO:0032868	Process	Response to insulin	IEA
GO:0033280	Process	Response to vitamin D	IEP	17023519
GO:0033883	Function	Pyridoxal phosphatase activity	IDA	2220817, 12162492
GO:0033883	Function	Pyridoxal phosphatase activity	IEA
GO:0034516	Process	Response to vitamin B6	IEA
GO:0036005	Process	Response to macrophage colony-stimulating factor	IEA
GO:0042822	Process	Pyridoxal phosphate metabolic process	IEA
GO:0043262	Function	ADP phosphatase activity	IEA
GO:0046677	Process	Response to antibiotic	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0050187	Function	Phosphoamidase activity	IEA
GO:0050187	Function	Phosphoamidase activity	ISS
GO:0051384	Process	Response to glucocorticoid	IEA
GO:0052732	Function	Phosphoethanolamine phosphatase activity	IDA	2220817
GO:0052732	Function	Phosphoethanolamine phosphatase activity	IEA
GO:0055062	Process	Phosphate ion homeostasis	IEA
GO:0055074	Process	Calcium ion homeostasis	IDA	28592560
GO:0055074	Process	Calcium ion homeostasis	IEA
GO:0065010	Component	Extracellular membrane-bounded organelle	IEA
GO:0065010	Component	Extracellular membrane-bounded organelle	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867, 23533145
GO:0071529	Process	Cementum mineralization	IEA
GO:0098552	Component	Side of membrane	IEA
GO:0120162	Process	Positive regulation of cold-induced thermogenesis	IEA
GO:0120162	Process	Positive regulation of cold-induced thermogenesis	ISS
GO:0140651	Process	Futile creatine cycle	IEA
GO:0140928	Process	Inhibition of non-skeletal tissue mineralization	IEA
GO:1904383	Process	Response to sodium phosphate	IEA

MIM	HGNC	e!Ensembl
171760	438	ENSG00000162551

Protein

UniProt ID

P05186

Protein name

Alkaline phosphatase, tissue-nonspecific isozyme (AP-TNAP) (TNS-ALP) (TNSALP) (EC 3.1.3.1) (Alkaline phosphatase liver/bone/kidney isozyme) (Phosphoamidase) (Phosphocreatine phosphatase) (EC 3.9.1.1)

Protein function

Alkaline phosphatase that metabolizes various phosphate compounds and plays a key role in skeletal mineralization and adaptive thermogenesis (PubMed:12162492, PubMed:23688511, PubMed:25982064). Has broad substrate specificity and can hydrolyze a

PDB

7YIV , 7YIW , 7YIX

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00245	Alk_phosphatase	51 → 490	Alkaline phosphatase	Domain

Sequence

MISPFLVLAIGTCLTNSLVPEKEKDPKYWRDQAQETLKYALELQKLNTNVAKNVIMFLGD
GMGVSTVTAARILKGQLHHNPGEETRLEMDKFPFVALSKTYNTNAQVPDSAGTATAYLCG
VKANEGTVGVSAATERSRCNTTQGNEVTSILRWAKDAGKSVGIVTTTRVNHATPSAAYAH
SADRDWYSDNEMPPEALSQGCKDIAYQLMHNIRDIDVIMGGGRKYMYPKNKTDVEYESDE
KARGTRLDGLDLVDTWKSFKPRYKHSHFIWNRTELLTLDPHNVDYLLGLFEPGDMQYELN
RNNVTDPSLSEMVVVAIQILRKNPKGFFLLVEGGRIDHGHHEGKAKQALHEAVEMDRAIG
QAGSLTSSEDTLTVVTADHSHVFTFGGYTPRGNSIFGLAPMLSDTDKKPFTAILYGNGPG
YKVVGGERENVSMVDYAHNNYQAQSAVPLRHETHGGEDVAVFSKGPMAHLLHGVHEQNYV
PHVMAYAACIGANLGHCAPASSAGSLAAGPLLLALALYPLSVLF

Sequence length

524

Interactions

View interactions

	KEGG		Reactome
	Thiamine metabolism Folate biosynthesis Metabolic pathways Biosynthesis of cofactors		Post-translational modification: synthesis of GPI-anchored proteins

Show/Hide Causal Diseases (3)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Hypophosphatasia	adult hypophosphatasia, infantile hypophosphatasia, Childhood hypophosphatasia, hypophosphatasia	rs121918009, rs121918000, rs769948289, rs754826836, rs121918018, rs1384701659, rs1413274209, rs121918011, rs121918003, rs771540767, rs1644755212, rs121918020, rs1054159992, rs766076920, rs764322898 View all (78 more)	N/A
Osteogenesis Imperfecta	osteogenesis imperfecta	rs781272386, rs763159520, rs121918009, rs121918011, rs1057521085, rs121918007, rs753338851, rs121918019, rs121918002, rs371243939	N/A
ODONTOHYPOPHOSPHATASIA	odontohypophosphatasia	rs121918011, rs763159520, rs121918007, rs121918013, rs121918015, rs121918018	N/A

Show/Hide Unknown Diseases (2)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Microcephaly	microcephaly	N/A	N/A	ClinVar
Urolithiasis	Urolithiasis	N/A	N/A	GWAS

Show/Hide Text Mining Associations (79)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Acid Phosphatase Deficiency	Associate	39276275
Appendicitis	Stimulate	27417541
Arthralgia	Associate	36514157
Asthma	Associate	31903716
Back Pain	Associate	32572521
Bone Diseases	Associate	29659871, 33191482, 36361766, 37107680
Bone Diseases Metabolic	Associate	32572521, 36361766
Calcinosis	Associate	32375544, 39755217
Campomelic Dysplasia	Associate	26432670
Carcinoma Renal Cell	Associate	34222474
Cardiovascular Diseases	Associate	30837522
Cartilage Diseases	Associate	19723327
Chondrocalcinosis	Associate	36514157
Chronic Kidney Disease Mineral and Bone Disorder	Inhibit	36414794
Chronic recurrent multifocal osteomyelitis	Associate	19335222
COVID 19	Associate	34582497, 37814484
Digestive System Diseases	Associate	38234425
Disease	Associate	22322541, 30929401
Femoral Fractures	Associate	35229197
Fetal Diseases	Associate	36427976
Foot Deformities	Associate	34097127
Fractures Bone	Associate	25736332, 31267001, 36414794, 36514157
Fractures Multiple	Associate	18219546
Fractures Stress	Associate	32066479
Genetic Diseases Inborn	Associate	16803637
Genital Diseases Female	Associate	29659871
Glioblastoma	Associate	31137733
Graves Ophthalmopathy	Associate	38130930
Growth Disorders	Associate	32772198
HEM dysplasia	Associate	32752906
Hip Fractures	Associate	22322541
Hypercalcemia	Stimulate	40409424
Hypophosphatasia	Inhibit	12674323, 17384481, 36414794
Hypophosphatasia	Associate	1409720, 16803637, 1689104, 17241478, 17384481, 18219546, 18559907, 19232125, 19335222, 19500388, 22014174, 22322541, 22394703, 22397652, 22703652 View all (78 more)
Hypophosphatasia Adult	Associate	29724887, 31014398, 31267001, 32572521, 33191482, 34097127, 35498405
Hypophosphatasia Infantile	Associate	27086862
Immunologic Deficiency Syndromes	Inhibit	9403706
Inflammation	Associate	17241478
Kidney Calculi	Associate	26272126
Late Onset Disorders	Associate	31793067
Leukemia Promyelocytic Acute	Associate	7780146
Lung Diseases	Associate	28663156
Malformations of Cortical Development	Associate	34673643
Mucocutaneous Lymph Node Syndrome	Associate	35755167, 36829193
Muscle Hypotonia	Associate	36361766
Muscle Weakness	Associate	38307176
Muscular Diseases	Associate	33191482
Musculoskeletal Pain	Associate	32066479, 32572521
Neoplasm Metastasis	Associate	34511489
Neoplasms	Associate	38553309
Nephrolithiasis	Associate	31754202
Nephrolithiasis Calcium Oxalate	Associate	31754202, 35741705
Obesity	Stimulate	30837522
Odontohypophosphatasia	Associate	23791648, 37408354
Osteoarthritis	Associate	23671648, 36142513
Osteoarthritis Knee	Associate	24123110
Osteogenesis Imperfecta	Associate	26432670, 37758163
Osteomalacia	Associate	19335222, 22322541, 24064686, 24123110, 25736332, 38307176
Osteoporosis	Associate	23353624, 29568943, 31014398, 31793067
Osteosarcoma	Associate	32173717
Ovarian Diseases	Associate	29659871
Pain	Associate	19335222, 36514157
Peeling Skin Syndrome	Associate	22322541
Periarthritis	Associate	24123110
Prostatic Neoplasms Castration Resistant	Associate	31136607
Prostatitis	Associate	17241478
Renal Insufficiency	Associate	25736332
Respiratory Insufficiency	Associate	30929401, 36361766
Rickets	Associate	19335222, 24123110, 38307176
Spondylitis Ankylosing	Associate	17195227
Spondylocostal dysostosis autosomal recessive	Associate	32572521
Stomatognathic Diseases	Associate	29659871, 36514157
Subarachnoid Hemorrhage	Associate	34542421
Tooth Abnormalities	Associate	23791648, 31267001, 32066479
Tooth Diseases	Associate	33191482
Tooth Injuries	Associate	32572521, 37408354
Tooth Loss	Associate	24123110, 26783040, 32772198, 38307176
Vaginosis Bacterial	Associate	34097127, 34438404, 38307176
Vascular Calcification	Associate	26418500

ALPL (alkaline phosphatase, biomineralization associated)