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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	5264
Gene name Gene Name - the full gene name approved by the HGNC.	Phytanoyl-CoA 2-hydroxylase
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	PHYH
Synonyms (NCBI Gene) Gene synonyms aliases	LN1, LNAP1, PAHX, PHYH1, RD
Chromosome Chromosome number	10
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	10p13
Summary Summary of gene provided in NCBI Entrez Gene.	This gene is a member of the PhyH family and encodes a peroxisomal protein that is involved in the alpha-oxidation of 3-methyl branched fatty acids. Specifically, this protein converts phytanoyl-CoA to 2-hydroxyphytanoyl-CoA. Mutations in this gene have b

Show/Hide all(22)

SNP ID	Visualize variation	Clinical significance	Consequence
rs28939672	G>A,T	Pathogenic	Intron variant, coding sequence variant, missense variant, stop gained
rs62619919	C>T	Conflicting-interpretations-of-pathogenicity, benign-likely-benign, benign, likely-pathogenic	Missense variant, coding sequence variant
rs104894173	C>T	Pathogenic	Intron variant, missense variant, coding sequence variant
rs104894174	C>T	Pathogenic	Missense variant, coding sequence variant
rs104894178	G>A	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs104894179	T>G	Pathogenic	Missense variant, coding sequence variant
rs115198308	C>A,T	Uncertain-significance, benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs140995522	G>A,C,T	Conflicting-interpretations-of-pathogenicity	Intron variant
rs143957922	G>A,C,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Intron variant, synonymous variant, missense variant, coding sequence variant
rs145404396	G>A,C	Likely-pathogenic	5 prime UTR variant, missense variant, coding sequence variant
rs150631501	T>C	Conflicting-interpretations-of-pathogenicity, benign	Coding sequence variant, intron variant, synonymous variant, 5 prime UTR variant
rs201499815	C>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-pathogenic	Intron variant
rs201578674	T>C	Pathogenic-likely-pathogenic, pathogenic	Splice acceptor variant
rs201979258	G>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, intron variant, missense variant
rs566116760	->GAT	Likely-benign, likely-pathogenic, conflicting-interpretations-of-pathogenicity	Inframe insertion, coding sequence variant
rs730882058	A>-	Pathogenic	Coding sequence variant, 5 prime UTR variant, frameshift variant
rs752028596	C>G,T	Likely-pathogenic	Coding sequence variant, intron variant, missense variant
rs797045100	CA>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1057272016	C>G	Pathogenic	Splice acceptor variant
rs1057520786	G>T	Pathogenic	Stop gained, coding sequence variant
rs1554784939	A>G	Likely-pathogenic	Splice donor variant
rs1554785113	G>A	Pathogenic	5 prime UTR variant, stop gained, coding sequence variant

Show/Hide all(117)

miRTarBase ID	miRNA	Experiments	Reference
MIRT050505	hsa-miR-20a-5p	CLASH	23622248
MIRT1232567	hsa-miR-3653	CLIP-seq
MIRT1232568	hsa-miR-3658	CLIP-seq
MIRT1232569	hsa-miR-4666-5p	CLIP-seq
MIRT1232570	hsa-miR-570	CLIP-seq
MIRT1232571	hsa-miR-1323	CLIP-seq
MIRT1232572	hsa-miR-218	CLIP-seq
MIRT1232573	hsa-miR-3591-3p	CLIP-seq
MIRT1232574	hsa-miR-4289	CLIP-seq
MIRT1232575	hsa-miR-548o	CLIP-seq
MIRT2295617	hsa-miR-1267	CLIP-seq
MIRT1232571	hsa-miR-1323	CLIP-seq
MIRT1232572	hsa-miR-218	CLIP-seq
MIRT1232573	hsa-miR-3591-3p	CLIP-seq
MIRT1232574	hsa-miR-4289	CLIP-seq
MIRT2295618	hsa-miR-4652-3p	CLIP-seq
MIRT2295619	hsa-miR-488	CLIP-seq
MIRT1232575	hsa-miR-548o	CLIP-seq
MIRT2295620	hsa-miR-653	CLIP-seq
MIRT2295621	hsa-miR-659	CLIP-seq
MIRT2593212	hsa-miR-1257	CLIP-seq
MIRT2295617	hsa-miR-1267	CLIP-seq
MIRT2593213	hsa-miR-1275	CLIP-seq
MIRT2593214	hsa-miR-1282	CLIP-seq
MIRT2593215	hsa-miR-216b	CLIP-seq
MIRT2593216	hsa-miR-28-3p	CLIP-seq
MIRT2593217	hsa-miR-3140-3p	CLIP-seq
MIRT2593218	hsa-miR-3148	CLIP-seq
MIRT2593219	hsa-miR-3163	CLIP-seq
MIRT2593220	hsa-miR-337-3p	CLIP-seq
MIRT2593221	hsa-miR-361-5p	CLIP-seq
MIRT1232567	hsa-miR-3653	CLIP-seq
MIRT1232568	hsa-miR-3658	CLIP-seq
MIRT2593222	hsa-miR-425	CLIP-seq
MIRT2593223	hsa-miR-4260	CLIP-seq
MIRT2593224	hsa-miR-4273	CLIP-seq
MIRT2593225	hsa-miR-4282	CLIP-seq
MIRT2593226	hsa-miR-4307	CLIP-seq
MIRT2593227	hsa-miR-4506	CLIP-seq
MIRT2593228	hsa-miR-452	CLIP-seq
MIRT2593229	hsa-miR-4525	CLIP-seq
MIRT2295618	hsa-miR-4652-3p	CLIP-seq
MIRT2593230	hsa-miR-4665-5p	CLIP-seq
MIRT1232569	hsa-miR-4666-5p	CLIP-seq
MIRT2593231	hsa-miR-4668-5p	CLIP-seq
MIRT2593232	hsa-miR-4676-3p	CLIP-seq
MIRT2593233	hsa-miR-4677-5p	CLIP-seq
MIRT2593234	hsa-miR-4693-5p	CLIP-seq
MIRT2593235	hsa-miR-4715-3p	CLIP-seq
MIRT2593236	hsa-miR-4723-5p	CLIP-seq
MIRT2593237	hsa-miR-4777-5p	CLIP-seq
MIRT2593238	hsa-miR-4780	CLIP-seq
MIRT2593239	hsa-miR-4789-5p	CLIP-seq
MIRT2295619	hsa-miR-488	CLIP-seq
MIRT2593240	hsa-miR-499-3p	CLIP-seq
MIRT2593241	hsa-miR-499a-3p	CLIP-seq
MIRT2593242	hsa-miR-518d-5p	CLIP-seq
MIRT2593243	hsa-miR-519b-5p	CLIP-seq
MIRT2593244	hsa-miR-519c-5p	CLIP-seq
MIRT2593245	hsa-miR-520c-5p	CLIP-seq
MIRT2593246	hsa-miR-526a	CLIP-seq
MIRT2593247	hsa-miR-544	CLIP-seq
MIRT2593248	hsa-miR-548c-3p	CLIP-seq
MIRT1232570	hsa-miR-570	CLIP-seq
MIRT2593249	hsa-miR-576-3p	CLIP-seq
MIRT2593250	hsa-miR-625	CLIP-seq
MIRT2593251	hsa-miR-629	CLIP-seq
MIRT2295620	hsa-miR-653	CLIP-seq
MIRT2295621	hsa-miR-659	CLIP-seq
MIRT2593252	hsa-miR-938	CLIP-seq
MIRT2593212	hsa-miR-1257	CLIP-seq
MIRT2295617	hsa-miR-1267	CLIP-seq
MIRT2593213	hsa-miR-1275	CLIP-seq
MIRT2593214	hsa-miR-1282	CLIP-seq
MIRT2593215	hsa-miR-216b	CLIP-seq
MIRT2593216	hsa-miR-28-3p	CLIP-seq
MIRT2593217	hsa-miR-3140-3p	CLIP-seq
MIRT2593218	hsa-miR-3148	CLIP-seq
MIRT2593219	hsa-miR-3163	CLIP-seq
MIRT2593220	hsa-miR-337-3p	CLIP-seq
MIRT2593221	hsa-miR-361-5p	CLIP-seq
MIRT1232567	hsa-miR-3653	CLIP-seq
MIRT1232568	hsa-miR-3658	CLIP-seq
MIRT2593222	hsa-miR-425	CLIP-seq
MIRT2593223	hsa-miR-4260	CLIP-seq
MIRT2593224	hsa-miR-4273	CLIP-seq
MIRT2593225	hsa-miR-4282	CLIP-seq
MIRT2593226	hsa-miR-4307	CLIP-seq
MIRT2593227	hsa-miR-4506	CLIP-seq
MIRT2593229	hsa-miR-4525	CLIP-seq
MIRT2295618	hsa-miR-4652-3p	CLIP-seq
MIRT2593230	hsa-miR-4665-5p	CLIP-seq
MIRT1232569	hsa-miR-4666-5p	CLIP-seq
MIRT2593231	hsa-miR-4668-5p	CLIP-seq
MIRT2593233	hsa-miR-4677-5p	CLIP-seq
MIRT2593235	hsa-miR-4715-3p	CLIP-seq
MIRT2593236	hsa-miR-4723-5p	CLIP-seq
MIRT2593237	hsa-miR-4777-5p	CLIP-seq
MIRT2593238	hsa-miR-4780	CLIP-seq
MIRT2593239	hsa-miR-4789-5p	CLIP-seq
MIRT2295619	hsa-miR-488	CLIP-seq
MIRT2593240	hsa-miR-499-3p	CLIP-seq
MIRT2593241	hsa-miR-499a-3p	CLIP-seq
MIRT2593242	hsa-miR-518d-5p	CLIP-seq
MIRT2593243	hsa-miR-519b-5p	CLIP-seq
MIRT2593244	hsa-miR-519c-5p	CLIP-seq
MIRT2593245	hsa-miR-520c-5p	CLIP-seq
MIRT2593246	hsa-miR-526a	CLIP-seq
MIRT2593247	hsa-miR-544	CLIP-seq
MIRT2593248	hsa-miR-548c-3p	CLIP-seq
MIRT1232570	hsa-miR-570	CLIP-seq
MIRT2593249	hsa-miR-576-3p	CLIP-seq
MIRT2593250	hsa-miR-625	CLIP-seq
MIRT2593251	hsa-miR-629	CLIP-seq
MIRT2295620	hsa-miR-653	CLIP-seq
MIRT2295621	hsa-miR-659	CLIP-seq
MIRT2593252	hsa-miR-938	CLIP-seq

Show/Hide all(26)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001561	Process	Fatty acid alpha-oxidation	IBA
GO:0001561	Process	Fatty acid alpha-oxidation	IDA	9326939, 16186124
GO:0001561	Process	Fatty acid alpha-oxidation	IEA
GO:0001561	Process	Fatty acid alpha-oxidation	IEA
GO:0003824	Function	Catalytic activity	IEA
GO:0005515	Function	Protein binding	IPI	9326939, 10051602, 16189514, 25416956, 25910212, 31515488, 32296183, 32814053
GO:0005777	Component	Peroxisome	IDA	9326939
GO:0005777	Component	Peroxisome	IEA
GO:0005782	Component	Peroxisomal matrix	TAS
GO:0005829	Component	Cytosol	TAS
GO:0006103	Process	2-oxoglutarate metabolic process	IDA	16186124
GO:0006631	Process	Fatty acid metabolic process	IEA
GO:0006720	Process	Isoprenoid metabolic process	IDA	11555634
GO:0008198	Function	Ferrous iron binding	IDA	9326939, 10744784, 11555634, 16186124
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0019606	Process	2-oxobutyrate catabolic process	IEA
GO:0031406	Function	Carboxylic acid binding	IDA	16186124
GO:0031418	Function	L-ascorbic acid binding	IDA	10744784
GO:0031418	Function	L-ascorbic acid binding	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0048244	Function	Phytanoyl-CoA dioxygenase activity	IBA
GO:0048244	Function	Phytanoyl-CoA dioxygenase activity	IDA	9326939, 10744784, 11555634, 16186124
GO:0048244	Function	Phytanoyl-CoA dioxygenase activity	IEA
GO:0051213	Function	Dioxygenase activity	IEA
GO:0097089	Process	Methyl-branched fatty acid metabolic process	IDA	10744784
GO:0097731	Component	9+0 non-motile cilium	IDA	29257953

MIM	HGNC	e!Ensembl
602026	8940	ENSG00000107537

Protein

UniProt ID

O14832

Protein name

Phytanoyl-CoA dioxygenase, peroxisomal (EC 1.14.11.18) (Phytanic acid oxidase) (Phytanoyl-CoA alpha-hydroxylase) (PhyH)

Protein function

Catalyzes the 2-hydroxylation of not only racemic phytanoyl-CoA and the isomers of 3-methylhexadecanoyl-CoA, but also a variety of other mono-branched 3-methylacyl-CoA esters (with a chain length of at least seven carbon atoms) and straight-chai

PDB

2A1X

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF05721	PhyH	61 → 277	Phytanoyl-CoA dioxygenase (PhyH)	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in liver, kidney, and T-cells, but not in spleen, brain, heart, lung and skeletal muscle.

Sequence

MEQLRAAARLQIVLGHLGRPSAGAVVAHPTSGTISSASFHPQQFQYTLDNNVLTLEQRKF
YEENGFLVIKNLVPDADIQRFRNEFEKICRKEVKPLGLTVMRDVTISKSEYAPSEKMITK
VQDFQEDKELFRYCTLPEILKYVECFTGPNIMAMHTMLINKPPDSGKKTSRHPLHQDLHY
FPFRPSDLIVCAWTAMEHISRNNGCLVVLPGTHKGSLKPHDYPKWEGGVNKMFHGIQDYE
ENKARVHLVMEKGDTVFFHPLLIHGSGQNKTQGFRKAISCHFASADCHYIDVKGTSQENI
EKEVVGIAHKFFGAENSVNLKDIWMFRARLVKGERTNL

Sequence length

338

Interactions

View interactions

	KEGG		Reactome
	Peroxisome		Alpha-oxidation of phytanate Peroxisomal protein import

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
Refsum Disease	refsum disease, adult, 1	rs104894178, rs201578674, rs730882058, rs104894179, rs28939672, rs104894173, rs104894174	N/A
retinal dystrophy	Retinal dystrophy	rs144169488, rs201578674	N/A
Retinitis Pigmentosa	retinitis pigmentosa	rs104894178, rs201578674	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.
Optic Atrophy	optic atrophy	N/A	N/A	ClinVar
Vitamin D-Dependent Rickets	Vitamin D-dependent rickets type II with alopecia	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (8)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Carcinoma Hepatocellular	Associate	11304581
Carcinoma Renal Cell	Inhibit	33468235
Crohn Disease	Associate	37543814
Dysbiosis	Associate	37543814
Neoplastic Syndromes Hereditary	Associate	31513212
Neuroferritinopathy	Associate	31513212
Orofacial Cleft 1	Associate	27229527
Refsum Disease	Associate	12522768, 15930519, 16186124

PHYH (phytanoyl-CoA 2-hydroxylase)