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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	85007
Gene name	5-phosphohydroxy-L-lysine phospho-lyase
Gene symbol	PHYKPL
Synonyms (NCBI Gene)	AGXT2L2PHLU
Chromosome	5
Chromosome location	5q35.3
Summary	This is a nuclear gene encoding a mitochondrial enzyme that catalyzes the conversion of 5-phosphonooxy-L-lysine to ammonia, inorganic phosphate, and 2-aminoadipate semialdehyde. Mutations in this gene may cause phosphohydroxylysinuria. Alternative splicin

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SNP ID	Visualize variation	Clinical significance	Consequence
rs142181517	T>A	Pathogenic	Genic downstream transcript variant, missense variant, coding sequence variant, non coding transcript variant
rs201105857	C>T	Pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant, non coding transcript variant, intron variant

Show/Hide all (38)

miRTarBase ID	miRNA	Experiments	Reference
MIRT459303	hsa-miR-1179	PAR-CLIP	23592263
MIRT459301	hsa-miR-4695-5p	PAR-CLIP	23592263
MIRT459302	hsa-miR-4779	PAR-CLIP	23592263
MIRT459300	hsa-miR-6732-5p	PAR-CLIP	23592263
MIRT459299	hsa-miR-765	PAR-CLIP	23592263
MIRT459298	hsa-miR-6752-5p	PAR-CLIP	23592263
MIRT459297	hsa-miR-6842-5p	PAR-CLIP	23592263
MIRT459296	hsa-miR-7110-5p	PAR-CLIP	23592263
MIRT459295	hsa-miR-4651	PAR-CLIP	23592263
MIRT459294	hsa-miR-608	PAR-CLIP	23592263
MIRT459293	hsa-miR-197-5p	PAR-CLIP	23592263
MIRT459292	hsa-miR-3132	PAR-CLIP	23592263
MIRT459291	hsa-miR-6756-5p	PAR-CLIP	23592263
MIRT459290	hsa-miR-6766-5p	PAR-CLIP	23592263
MIRT459289	hsa-miR-6769a-5p	PAR-CLIP	23592263
MIRT459288	hsa-miR-6769b-5p	PAR-CLIP	23592263
MIRT459287	hsa-miR-1258	PAR-CLIP	23592263
MIRT459285	hsa-miR-4266	PAR-CLIP	23592263
MIRT459286	hsa-miR-1229-5p	PAR-CLIP	23592263
MIRT459303	hsa-miR-1179	PAR-CLIP	23592263
MIRT459301	hsa-miR-4695-5p	PAR-CLIP	23592263
MIRT459302	hsa-miR-4779	PAR-CLIP	23592263
MIRT459300	hsa-miR-6732-5p	PAR-CLIP	23592263
MIRT459299	hsa-miR-765	PAR-CLIP	23592263
MIRT459298	hsa-miR-6752-5p	PAR-CLIP	23592263
MIRT459297	hsa-miR-6842-5p	PAR-CLIP	23592263
MIRT459296	hsa-miR-7110-5p	PAR-CLIP	23592263
MIRT459295	hsa-miR-4651	PAR-CLIP	23592263
MIRT459294	hsa-miR-608	PAR-CLIP	23592263
MIRT459293	hsa-miR-197-5p	PAR-CLIP	23592263
MIRT459292	hsa-miR-3132	PAR-CLIP	23592263
MIRT459291	hsa-miR-6756-5p	PAR-CLIP	23592263
MIRT459290	hsa-miR-6766-5p	PAR-CLIP	23592263
MIRT459289	hsa-miR-6769a-5p	PAR-CLIP	23592263
MIRT459288	hsa-miR-6769b-5p	PAR-CLIP	23592263
MIRT459287	hsa-miR-1258	PAR-CLIP	23592263
MIRT459285	hsa-miR-4266	PAR-CLIP	23592263
MIRT459286	hsa-miR-1229-5p	PAR-CLIP	23592263

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GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	21044950, 25416956, 29892012, 31515488
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	IEA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0008483	Function	Transaminase activity	IEA
GO:0016829	Function	Lyase activity	IEA
GO:0030170	Function	Pyridoxal phosphate binding	IEA
GO:0042802	Function	Identical protein binding	IPI	16189514, 25416956, 31515488, 32296183

MIM	HGNC	e!Ensembl
614683	28249	ENSG00000175309

Q8IUZ5

Protein name

5-phosphohydroxy-L-lysine phospho-lyase (EC 4.2.3.134) (Alanine--glyoxylate aminotransferase 2-like 2)

Protein function

Catalyzes the pyridoxal-phosphate-dependent breakdown of 5-phosphohydroxy-L-lysine, converting it to ammonia, inorganic phosphate and 2-aminoadipate semialdehyde.

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00202	Aminotran_3	28 → 433	Aminotransferase class-III	Domain

Sequence

MAADQRPKADTLALRQRLISSSCRLFFPEDPVKIVRAQGQYMYDEQGAEYIDCISNVAHV
GHCHPLVVQAAHEQNQVLNTNSRYLHDNIVDYAQRLSETLPEQLCVFYFLNSGSEANDLA
LRLARHYTGHQDVVVLDHAYHGHLSSLIDISPYKFRNLDGQKEWVHVAPLPDTYRGPYRE
DHPNPAMAYANEVKRVVSSAQEKGRKIAAFFAESLPSVGGQIIPPAGYFSQVAEHIRKAG
GVFVADEIQVGFGRVGKHFWAFQLQGKDFVPDIVTMGKSIGNGHPVACVAATQPVARAFE
ATGVEYFNTFGGSPVSCAVGLAVLNVLEKEQLQDHATSVGSFLMQLLGQQKIKHPIVGDV
RGVGLFIGVDLIKDEATRTPATEEAAYLVSRLKENYVLLSTDGPGRNILKFKPPMCFSLD
NARQVVAKLDAILTDMEEKVRSCETLRLQP

Sequence length

450

Interactions

View interactions

	KEGG		Reactome
	Lysine degradation Metabolic pathways		Collagen degradation Lysine catabolism

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (8)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Cervical cancer	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DENTAL CARIES	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLOMERULONEPHRITIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Phosphohydroxylysinuria	no classifications from unflagged records; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PHYKPL-related disorder	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ULCERATIVE COLITIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (6)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Leukemia, Myelocytic, Acute	Leukemia	GWASCAT_DG	27903959		★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	Pubtator	40148931	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Phosphohydroxylysinuria	Phosphohydroxylysinuria	BEFREE	22241472, 23242558		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Phosphohydroxylysinuria	Phosphohydroxylysinuria	UNIPROT_DG	23242558		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Phosphohydroxylysinuria	Phosphohydroxylysinuria	GENOMICS_ENGLAND_DG	27604308		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Phosphohydroxylysinuria	Phosphohydroxylysinuria	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

PHYKPL (5-phosphohydroxy-L-lysine phospho-lyase)