PIGV (phosphatidylinositol glycan anchor biosynthesis class V)

Gene

• Entrez ID: 55650
• Gene name: Phosphatidylinositol glycan anchor biosynthesis class V
• Gene symbol: PIGV
• Synonyms (NCBI Gene): GPI-MT-II, HPMRS1, PIG-V
• Chromosome: 1
• Chromosome location: 1p36.11
• Summary: This gene encodes a mannosyltransferase enzyme involved in the biosynthesis of glycosylphosphatidylinositol (GPI). GPI is a complex glycolipid that functions as a membrane anchor for many proteins and plays a role in multiple cellular processes including

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs139073416	C>A,T	Likely-pathogenic, pathogenic	Non coding transcript variant, missense variant, intron variant, coding sequence variant
rs142192097	A>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, intron variant, 5 prime UTR variant, non coding transcript variant, missense variant
rs146969255	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, non coding transcript variant
rs148662665	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity, likely-benign	5 prime UTR variant, non coding transcript variant, synonymous variant, coding sequence variant, intron variant
rs267606951	A>C,G	Pathogenic	Intron variant, missense variant, coding sequence variant, non coding transcript variant
rs267606952	C>A	Pathogenic	Intron variant, missense variant, coding sequence variant, non coding transcript variant
rs376328153	C>A	Pathogenic	Coding sequence variant, missense variant, intron variant, non coding transcript variant
rs387907023	G>A	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant, intron variant, non coding transcript variant
rs759988046	C>T	Likely-pathogenic	Missense variant, intron variant, coding sequence variant, non coding transcript variant
rs766452597	A>G	Likely-pathogenic	Non coding transcript variant, intron variant, coding sequence variant, missense variant
rs774605091	T>C	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs1418108487	->A	Likely-pathogenic	Non coding transcript variant, intron variant, coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT535230	hsa-miR-552-3p	PAR-CLIP	22012620
MIRT535229	hsa-miR-3159	PAR-CLIP	22012620
MIRT535227	hsa-miR-6504-3p	PAR-CLIP	22012620
MIRT535228	hsa-miR-4740-3p	PAR-CLIP	22012620
MIRT535226	hsa-miR-6778-3p	PAR-CLIP	22012620
MIRT535225	hsa-miR-5095	PAR-CLIP	22012620
MIRT535224	hsa-miR-7151-3p	PAR-CLIP	22012620
MIRT535230	hsa-miR-552-3p	PAR-CLIP	22012620
MIRT535229	hsa-miR-3159	PAR-CLIP	22012620
MIRT535227	hsa-miR-6504-3p	PAR-CLIP	22012620
MIRT535228	hsa-miR-4740-3p	PAR-CLIP	22012620
MIRT535226	hsa-miR-6778-3p	PAR-CLIP	22012620
MIRT535225	hsa-miR-5095	PAR-CLIP	22012620
MIRT535224	hsa-miR-7151-3p	PAR-CLIP	22012620
MIRT1233605	hsa-miR-3157-3p	CLIP-seq
MIRT1233606	hsa-miR-4282	CLIP-seq
MIRT1233607	hsa-miR-4676-5p	CLIP-seq
MIRT1233608	hsa-miR-575	CLIP-seq
MIRT1233609	hsa-miR-874	CLIP-seq
MIRT1233610	hsa-miR-1827	CLIP-seq
MIRT1233611	hsa-miR-1915	CLIP-seq
MIRT1233612	hsa-miR-2467-3p	CLIP-seq
MIRT1233613	hsa-miR-2682	CLIP-seq
MIRT1233614	hsa-miR-4436b-3p	CLIP-seq
MIRT1233615	hsa-miR-449c	CLIP-seq
MIRT1233616	hsa-miR-4685-5p	CLIP-seq
MIRT1233617	hsa-miR-4726-3p	CLIP-seq
MIRT1233618	hsa-miR-922	CLIP-seq
MIRT2068757	hsa-miR-150	CLIP-seq
MIRT1233610	hsa-miR-1827	CLIP-seq
MIRT1233611	hsa-miR-1915	CLIP-seq
MIRT1233612	hsa-miR-2467-3p	CLIP-seq
MIRT1233613	hsa-miR-2682	CLIP-seq
MIRT2068758	hsa-miR-3117-5p	CLIP-seq
MIRT2068759	hsa-miR-365	CLIP-seq
MIRT2068760	hsa-miR-374a	CLIP-seq
MIRT2068761	hsa-miR-374b	CLIP-seq
MIRT2068762	hsa-miR-3942-3p	CLIP-seq
MIRT2068763	hsa-miR-4311	CLIP-seq
MIRT1233614	hsa-miR-4436b-3p	CLIP-seq
MIRT1233615	hsa-miR-449c	CLIP-seq
MIRT1233616	hsa-miR-4685-5p	CLIP-seq
MIRT2068764	hsa-miR-4713-5p	CLIP-seq
MIRT1233617	hsa-miR-4726-3p	CLIP-seq
MIRT2068765	hsa-miR-532-3p	CLIP-seq
MIRT2068766	hsa-miR-532-5p	CLIP-seq
MIRT2068767	hsa-miR-634	CLIP-seq
MIRT1233618	hsa-miR-922	CLIP-seq
MIRT2392512	hsa-miR-1200	CLIP-seq
MIRT2392513	hsa-miR-1251	CLIP-seq
MIRT2068757	hsa-miR-150	CLIP-seq
MIRT2068758	hsa-miR-3117-5p	CLIP-seq
MIRT2392514	hsa-miR-3660	CLIP-seq
MIRT2392515	hsa-miR-4526	CLIP-seq
MIRT2068764	hsa-miR-4713-5p	CLIP-seq
MIRT2068765	hsa-miR-532-3p	CLIP-seq
MIRT2392512	hsa-miR-1200	CLIP-seq
MIRT2593867	hsa-miR-1208	CLIP-seq
MIRT2068757	hsa-miR-150	CLIP-seq
MIRT2593868	hsa-miR-151-3p	CLIP-seq
MIRT1233610	hsa-miR-1827	CLIP-seq
MIRT1233611	hsa-miR-1915	CLIP-seq
MIRT2593869	hsa-miR-1972	CLIP-seq
MIRT1233612	hsa-miR-2467-3p	CLIP-seq
MIRT1233613	hsa-miR-2682	CLIP-seq
MIRT2068758	hsa-miR-3117-5p	CLIP-seq
MIRT2593870	hsa-miR-3673	CLIP-seq
MIRT2068760	hsa-miR-374a	CLIP-seq
MIRT2068761	hsa-miR-374b	CLIP-seq
MIRT2593871	hsa-miR-3934	CLIP-seq
MIRT2593872	hsa-miR-412	CLIP-seq
MIRT2593873	hsa-miR-4252	CLIP-seq
MIRT2593874	hsa-miR-4305	CLIP-seq
MIRT2068763	hsa-miR-4311	CLIP-seq
MIRT1233614	hsa-miR-4436b-3p	CLIP-seq
MIRT1233615	hsa-miR-449c	CLIP-seq
MIRT2593875	hsa-miR-4650-5p	CLIP-seq
MIRT1233616	hsa-miR-4685-5p	CLIP-seq
MIRT2068764	hsa-miR-4713-5p	CLIP-seq
MIRT1233617	hsa-miR-4726-3p	CLIP-seq
MIRT2593876	hsa-miR-4781-3p	CLIP-seq
MIRT2068765	hsa-miR-532-3p	CLIP-seq
MIRT2593877	hsa-miR-593	CLIP-seq
MIRT2593878	hsa-miR-607	CLIP-seq
MIRT2593879	hsa-miR-890	CLIP-seq
MIRT1233618	hsa-miR-922	CLIP-seq
MIRT2392512	hsa-miR-1200	CLIP-seq
MIRT2593867	hsa-miR-1208	CLIP-seq
MIRT2687881	hsa-miR-1269	CLIP-seq
MIRT2687882	hsa-miR-1269b	CLIP-seq
MIRT2687883	hsa-miR-1288	CLIP-seq
MIRT2687884	hsa-miR-147	CLIP-seq
MIRT2068757	hsa-miR-150	CLIP-seq
MIRT2593868	hsa-miR-151-3p	CLIP-seq
MIRT1233610	hsa-miR-1827	CLIP-seq
MIRT1233611	hsa-miR-1915	CLIP-seq
MIRT2593869	hsa-miR-1972	CLIP-seq
MIRT1233612	hsa-miR-2467-3p	CLIP-seq
MIRT1233613	hsa-miR-2682	CLIP-seq
MIRT2068758	hsa-miR-3117-5p	CLIP-seq
MIRT2687885	hsa-miR-3138	CLIP-seq
MIRT2068759	hsa-miR-365	CLIP-seq
MIRT2593870	hsa-miR-3673	CLIP-seq
MIRT2068760	hsa-miR-374a	CLIP-seq
MIRT2068761	hsa-miR-374b	CLIP-seq
MIRT2687886	hsa-miR-3911	CLIP-seq
MIRT2687887	hsa-miR-3919	CLIP-seq
MIRT2593871	hsa-miR-3934	CLIP-seq
MIRT2593872	hsa-miR-412	CLIP-seq
MIRT2593873	hsa-miR-4252	CLIP-seq
MIRT2593874	hsa-miR-4305	CLIP-seq
MIRT2068763	hsa-miR-4311	CLIP-seq
MIRT1233614	hsa-miR-4436b-3p	CLIP-seq
MIRT1233615	hsa-miR-449c	CLIP-seq
MIRT2687888	hsa-miR-4515	CLIP-seq
MIRT2593875	hsa-miR-4650-5p	CLIP-seq
MIRT1233616	hsa-miR-4685-5p	CLIP-seq
MIRT2068764	hsa-miR-4713-5p	CLIP-seq
MIRT1233617	hsa-miR-4726-3p	CLIP-seq
MIRT2687889	hsa-miR-4740-5p	CLIP-seq
MIRT2593876	hsa-miR-4781-3p	CLIP-seq
MIRT2687890	hsa-miR-4797-5p	CLIP-seq
MIRT2687891	hsa-miR-4800-5p	CLIP-seq
MIRT2068765	hsa-miR-532-3p	CLIP-seq
MIRT2068766	hsa-miR-532-5p	CLIP-seq
MIRT2687892	hsa-miR-581	CLIP-seq
MIRT2593877	hsa-miR-593	CLIP-seq
MIRT2687893	hsa-miR-600	CLIP-seq
MIRT2593878	hsa-miR-607	CLIP-seq
MIRT2068767	hsa-miR-634	CLIP-seq
MIRT2687894	hsa-miR-644	CLIP-seq
MIRT2593879	hsa-miR-890	CLIP-seq
MIRT1233618	hsa-miR-922	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000009	Function	Alpha-1,6-mannosyltransferase activity	IEA
GO:0000009	Function	Alpha-1,6-mannosyltransferase activity	IGI	15623507, 15720390
GO:0000009	Function	Alpha-1,6-mannosyltransferase activity	IMP	15623507
GO:0000030	Function	Mannosyltransferase activity	IBA
GO:0004376	Function	GPI mannosyltransferase activity	IEA
GO:0004376	Function	GPI mannosyltransferase activity	TAS
GO:0005515	Function	Protein binding	IPI	32814053
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IBA
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	15623507
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0006506	Process	GPI anchor biosynthetic process	IBA
GO:0006506	Process	GPI anchor biosynthetic process	IEA
GO:0006506	Process	GPI anchor biosynthetic process	IGI	15623507, 15720390
GO:0006506	Process	GPI anchor biosynthetic process	IMP	15623507
GO:0006506	Process	GPI anchor biosynthetic process	TAS
GO:0016020	Component	Membrane	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0031501	Component	Mannosyltransferase complex	IBA

Other IDs

• MIM: 610274
• HGNC: 26031
• e!Ensembl: ENSG00000060642

Protein

• UniProt ID: Q9NUD9
• Protein name: GPI alpha-1,6-mannosyltransferase 2 (EC 2.4.1.-) (GPI mannosyltransferase II) (GPI-MT-II) (Phosphatidylinositol-glycan biosynthesis class V protein) (PIG-V)
• Protein function: Alpha-1,6-mannosyltransferase that catalyzes the transfer of the second mannose, via an alpha-1,6 bond, from a dolichol-phosphate-mannose (Dol-P-Man) to the alpha-D-Man-(1->4)-alpha-D-GlcN-(1->6)-(1-radyl,2-acyl-sn-glycero-3-phospho)-2-acyl-inos
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF04188	Mannosyl_trans2	8 → 493	Mannosyltransferase (PIG-V)	Family

• Sequence:

  MWPQDPSRKEVLRFAVSCRILTLMLQALFNAIIPDHHAEAFSPPRLAPSGFVDQLVEGLL
  GGLSHWDAEHFLFIAEHGYLYEHNFAFFPGFPLALLVGTELLRPLRGLLSLRSCLLISVA
  SLNFLFFMLAAVALHDLGCLVLHCPHQSFYAALLFCLSPANVFLAAGYSEALFALLTFSA
  MGQLERGRVWTSVLLFAFATGVRSNGLVSVGFLMHSQCQGFFSSLTMLNPLRQLFKLMAS
  LFLSVFTLGLPFALFQYYAYTQFCLPGSARPIPEPLVQLAVDKGYRIAEGNEPPWCFWDV
  PLIYSYIQDVYWNVGFLKYYELKQVPNFLLAAPVAILVAWATWTYVTTHPWLCLTLGLQR
  SKNNKTLEKPDLGFLSPQVFVYVVHAAVLLLFGGLCMHVQVLTRFLGSSTPIMYWFPAHL
  LQDQEPLLRSLKTVPWKPLAEDSPPGQKVPRNPIMGLLYHWKTCSPVTRYILGYFLTYWL
  LGLLLHCNFLPWT

• Sequence length: 493

Pathways

KEGG:

Glycosylphosphatidylinositol (GPI)-anchor biosynthesis
Metabolic pathways

Reactome:

Synthesis of glycosylphosphatidylinositol (GPI)

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Hyperphosphatasia with intellectual disability syndrome 1	Likely pathogenic; Pathogenic	rs139073416, rs267606951, rs267606952, rs387907023, rs759988046, rs149690056	RCV000001347 RCV000001348 RCV000001349 RCV000001350 RCV000023806 RCV000660523 RCV001262427	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Hyperphosphatasia-intellectual disability syndrome	Likely pathogenic; Pathogenic	rs139073416	RCV000613584	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PIGV-related disorder	Likely pathogenic; Pathogenic	rs139073416	RCV004739277	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
DESBUQUOIS SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Elevated circulating alkaline phosphatase concentration	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERPHOSPHATASEMIA WITH INTELLECTUAL DISABILITY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERPHOSPHATASIA WITH IMPAIRED INTELLECTUAL DEVELOPMENT SYNDROME 1	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERPHOSPHATASIA WITH MENTAL RETARDATION	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Accessory nipple	Accessory Nipple	HPO_DG			★☆☆☆☆ Found in Text Mining only
Autistic behavior	Autism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Brachycephaly	Brachycephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebral cortical atrophy	Cerebral cortical atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Class III malocclusion	Malocclusion	HPO_DG			★☆☆☆☆ Found in Text Mining only
Clinodactyly	Clinodactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Clinodactyly of fingers	Clinodactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital anomaly of rectum	Congenital Anomaly Of Rectum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital anomaly of the kidney	Multicystic renal dysplasia	BEFREE	24129430		★☆☆☆☆ Found in Text Mining only
Congenital Epicanthus	Congenital Epicanthus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital Heart Defects	Congenital heart defects	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital malformation syndrome	Congenital Malformation Syndrome	BEFREE	24129430		★☆☆☆☆ Found in Text Mining only
Congenital pectus excavatum	Congenital Pectus Excavatum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	24129430	Associate	★☆☆☆☆ Found in Text Mining only
Esotropia	Esotropia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung Disease	BEFREE	21739589, 24129430		★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung disease	Pubtator	24129430, 29310717	Associate	★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hydronephrosis	Hydronephrosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hyperopia	Hyperopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hyperphosphatasemia with bone disease	Hyperphosphatasemia With Bone Disease	BEFREE	21704546		★☆☆☆☆ Found in Text Mining only
Hyperphosphatasia with Mental Retardation	Hyperphosphatasia With Mental Retardation	CLINVAR_DG	20802478, 21739589, 22228761, 22315194, 24129430		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hyperphosphatasia with Mental Retardation	Hyperphosphatasia with intellectual disability syndrome	Pubtator	22683086, 24129430, 24417746, 30813920	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hyperphosphatasia with Mental Retardation	Hyperphosphatasia With Mental Retardation	BEFREE	24129430, 24417746, 27177984, 28817240		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hyperphosphatasia with Mental Retardation	Hyperphosphatasia With Mental Retardation	ORPHANET_DG	24129430		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hyperphosphatasia with Mental Retardation	Hyperphosphatasia With Mental Retardation	GENOMICS_ENGLAND_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hyperphosphatasia with Mental Retardation	Hyperphosphatasia With Mental Retardation	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERPHOSPHATASIA WITH MENTAL RETARDATION SYNDROME 1	Hyperphosphatasia With Mental Retardation	UNIPROT_DG	20802478		★☆☆☆☆ Found in Text Mining only
HYPERPHOSPHATASIA WITH MENTAL RETARDATION SYNDROME 1	Hyperphosphatasia With Mental Retardation	GENOMICS_ENGLAND_DG	20802478, 24129430, 27604308		★☆☆☆☆ Found in Text Mining only
HYPERPHOSPHATASIA WITH MENTAL RETARDATION SYNDROME 1	Hyperphosphatasia With Mental Retardation	CLINVAR_DG	20802478, 21739589, 22228761, 22315194, 24129430		★☆☆☆☆ Found in Text Mining only
Hyperphosphatasia-intellectual disability syndrome	Hyperphosphatasia With Mental Retardation	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hypertension	Hypertension	Pubtator	32410228	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	20802478, 21739589, 23561847, 24129430		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	23561847, 24129430, 30813920	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mental Retardation	Mental retardation	BEFREE	20802478, 21739589		★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Moderate intellectual disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Oculomotor apraxia	Oculomotor apraxia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Oculovestibuloauditory syndrome	Oculovestibuloauditory Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Papillorenal syndrome	Papillorenal syndrome	Pubtator	24129430	Associate	★☆☆☆☆ Found in Text Mining only
Plagiocephaly	Plagiocephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Posteriorly rotated ear	Posteriorly Rotated Ear	HPO_DG			★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Seizures	Seizures	Pubtator	23561847	Associate	★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Severe intellectual disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Tonic - clonic seizures	Seizure	HPO_DG			★☆☆☆☆ Found in Text Mining only