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	5264
Gene name	Phytanoyl-CoA 2-hydroxylase
Gene symbol	PHYH
Synonyms (NCBI Gene)	LN1LNAP1PAHXPHYH1RD
Chromosome	10
Chromosome location	10p13
Summary	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

117

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

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

212

Show/Hide Causal Diseases (12)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Acute myeloid leukemia	Pathogenic	rs201578674	RCV005887356
Clear cell carcinoma of kidney	Pathogenic	rs201578674	RCV005887357
Familial cancer of breast	Pathogenic	rs201578674	RCV005887355
Hepatocellular carcinoma	Likely pathogenic	rs761927136	RCV005925434
PHYH-related disorder	Likely pathogenic; Pathogenic	rs970229634, rs201578674	RCV003402009 RCV003407301
Phytanic acid storage disease	Pathogenic; Likely pathogenic	rs767403321, rs1267819026, rs761927136, rs2131634446, rs2538643445, rs2538635262, rs1835618953, rs753115080, rs2538650629, rs2538635253, rs2538650783, rs1835606884, rs797045100, rs104894178, rs201578674 View all (22 more)	RCV003475158 RCV003475223 RCV003475265 RCV002272697 RCV002307941 RCV002307991 RCV002308280 RCV002309016 RCV002306832 RCV002310496 RCV003475488 RCV004571232 RCV000190614 RCV000665657 RCV000660487 RCV003473055 RCV003473056 RCV003475559 RCV003472441 RCV003472442 RCV003472443 RCV003472444 RCV003472445 RCV003472446 RCV003472447 RCV003472448 RCV003472449 RCV003472450 RCV003472451 RCV004574126 RCV004574177 RCV004574538 RCV000674886 RCV003473541 RCV001784612 RCV004761930 RCV003473811
REFSUM DISEASE, ADULT, 1	Likely pathogenic; Pathogenic	rs104894178, rs201578674, rs730882058, rs104894179, rs28939672, rs104894173, rs104894174	RCV000008018 RCV000008019 RCV000008021 RCV000008022 RCV000008024 RCV000008025 RCV000008026
Refsum syndrome	Likely pathogenic; Pathogenic	rs1057272016	RCV001003121
Retinal dystrophy	Pathogenic; Likely pathogenic	rs767403321, rs201578674, rs144169488	RCV004815758 RCV004814858 RCV001075231
Retinitis pigmentosa	Likely pathogenic; Pathogenic	rs104894178, rs201578674	RCV000505105 RCV001723551
Thyroid cancer, nonmedullary, 1	Pathogenic	rs201578674	RCV005887358
Uterine corpus endometrial carcinoma	Pathogenic	rs201578674	RCV005887359

Show/Hide Unknown Diseases (19)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Adrenocortical carcinoma, hereditary	Conflicting classifications of pathogenicity	rs62619919	RCV005892045
Cervical cancer	Benign; Likely benign	rs140995522	RCV005891784
Cholangiocarcinoma	Benign; Likely benign	rs140995522, rs140309981	RCV005891789 RCV005869279
Colon adenocarcinoma	Conflicting classifications of pathogenicity	rs201499815	RCV005892024
Gastric cancer	Conflicting classifications of pathogenicity; Benign; Likely benign	rs62619919, rs140995522	RCV005892046 RCV005891786
Intellectual disability	Conflicting classifications of pathogenicity	rs375508574, rs201936962	RCV005626305 RCV005626331
Lung cancer	Uncertain significance; Benign; Likely benign	rs116930123, rs140995522	RCV005891782 RCV005891790
Malignant lymphoma, large B-cell, diffuse	Benign; Likely benign	rs140309981	RCV005869277
Malignant tumor of esophagus	Conflicting classifications of pathogenicity; Uncertain significance	rs201499815, rs116930123	RCV005892026 RCV005891779
Melanoma	Conflicting classifications of pathogenicity; Uncertain significance	rs62619919, rs116930123	RCV005892047 RCV005891781
Nonpapillary renal cell carcinoma	Conflicting classifications of pathogenicity	rs201499815, rs62619919	RCV005892027 RCV005892044
Nonsyndromic cleft lip palate	Conflicting classifications of pathogenicity	rs62619919, rs566116760, rs145404396	RCV000755125 RCV000755124 RCV000755126
Optic atrophy	Conflicting classifications of pathogenicity	rs566116760	RCV004817741
Ovarian serous cystadenocarcinoma	Benign; Likely benign	rs150631501, rs140995522	RCV005891794 RCV005891787
Phytanoyl-CoA hydroxylase deficiency	Conflicting classifications of pathogenicity	rs201499815	RCV005361081
Sarcoma	Conflicting classifications of pathogenicity; Benign; Likely benign; Uncertain significance	rs201499815, rs150631501, rs116930123, rs140995522	RCV005892028 RCV005891793 RCV005891780 RCV005891785
Thymoma	Conflicting classifications of pathogenicity; Benign; Likely benign	rs201499815, rs140309981	RCV005892029 RCV005869278
Uterine carcinosarcoma	Benign; Likely benign	rs140995522	RCV005891788
Vitamin D-dependent rickets type II with alopecia	Conflicting classifications of pathogenicity	rs62619919	RCV001258288

Show/Hide Text Mining Associations (8)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)