PIGZ

phosphatidylinositol glycan anchor biosynthesis class Z, the group of Dolichyl D-mannosyl phosphate dependent mannosyltransferases|Phosphatidylinositol glycan anchor biosynthesis

Basic information

Region (hg38): 3:196946356-196969060

Links

ENSG00000119227 ∙ NCBI:80235 ∙ OMIM:611671 ∙ HGNC:30596 ∙ Uniprot:Q86VD9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PIGZ gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIGZ gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	2	7
missense			64	7		71
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	64	12	2

Variants in PIGZ

This is a list of pathogenic ClinVar variants found in the PIGZ region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-196947215-C-T		not specified	Uncertain significance (Jun 28, 2023)
3-196947294-T-C		not specified	Uncertain significance (Dec 16, 2021)
3-196947350-A-C		not specified	Uncertain significance (Feb 21, 2025)
3-196947366-C-T			Likely benign (Mar 01, 2025)
3-196947434-C-G		not specified	Uncertain significance (Jun 22, 2021)
3-196947434-C-T		not specified	Uncertain significance (Mar 07, 2024)
3-196947441-C-G		not specified	Uncertain significance (Sep 21, 2021)
3-196947444-C-A		not specified	Uncertain significance (Feb 22, 2023)
3-196947455-G-A		not specified	Uncertain significance (May 30, 2023)
3-196947459-C-T		not specified	Uncertain significance (Oct 13, 2023)
3-196947470-G-A		not specified	Uncertain significance (Jun 24, 2022)
3-196947477-G-A		not specified	Uncertain significance (Aug 13, 2021)
3-196947486-G-A		not specified	Uncertain significance (Feb 05, 2024)
3-196947489-G-A		not specified	Uncertain significance (Mar 25, 2024)
3-196947493-G-A			Benign (Nov 01, 2023)
3-196947496-C-G		not specified	Uncertain significance (Jan 02, 2025)
3-196947558-G-T		not specified	Uncertain significance (Nov 26, 2024)
3-196947570-C-G		not specified	Uncertain significance (Oct 28, 2024)
3-196947615-C-T		not specified	Uncertain significance (Mar 07, 2024)
3-196947621-G-C		not specified	Uncertain significance (Apr 06, 2023)
3-196947625-G-A			Likely benign (Sep 01, 2022)
3-196947630-C-T		not specified	Uncertain significance (Jun 26, 2023)
3-196947636-C-T		not specified	Uncertain significance (Jun 11, 2021)
3-196947677-G-A		not specified	Uncertain significance (Sep 12, 2023)
3-196947723-G-C		not specified	Uncertain significance (Jan 20, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIGZ	protein_coding	protein_coding	ENST00000412723	2	22718

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000127	0.844	125593	0	155	125748	0.000616

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0441	337	335	1.01	0.0000197	3628
Missense in Polyphen		103	111.4	0.92463		1327
Synonymous	-2.15	192	158	1.22	0.00000962	1348
Loss of Function	1.38	10	16.0	0.627	8.19e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00147	0.00146
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.00141	0.00141
Finnish	0.0000949	0.0000924
European (Non-Finnish)	0.000576	0.000571
Middle Eastern	0.00141	0.00141
South Asian	0.000491	0.000490
Other	0.00132	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mannosyltransferase involved in glycosylphosphatidylinositol-anchor biosynthesis. Transfers a fourth mannose to some trimannosyl-GPIs during GPI precursor assembly. The presence of a fourth mannose in GPI is facultative and only scarcely detected, suggesting that it only exists in some tissues. {ECO:0000269|PubMed:15208306}.
• Pathway: Glycosylphosphatidylinositol (GPI)-anchor biosynthesis - Homo sapiens (human);Synthesis of glycosylphosphatidylinositol (GPI);Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.0973

Intolerance Scores

• loftool: 0.805
• rvis_EVS: 0.29
• rvis_percentile_EVS: 71.62

Haploinsufficiency Scores

• pHI: 0.0515
• hipred: N
• hipred_score: 0.146
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0494

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pigz

Gene ontology

• Biological process: GPI anchor biosynthetic process;preassembly of GPI anchor in ER membrane;mannosylation
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: alpha-1,2-mannosyltransferase activity;mannosyltransferase activity