PIGX

phosphatidylinositol glycan anchor biosynthesis class X, the group of Phosphatidylinositol glycan anchor biosynthesis

Basic information

Region (hg38): 3:196639775-196736007

Links

ENSG00000163964 ∙ NCBI:54965 ∙ OMIM:610276 ∙ HGNC:26046 ∙ Uniprot:Q8TBF5 ∙ 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 PIGX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIGX 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				1		1
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in PIGX

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

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

Position	Type	Phenotype	Significance	ClinVar
3-196654568-T-C		Seizures, early-onset, with neurodegeneration and brain calcifications	Pathogenic (May 15, 2020)
3-196654604-G-A		Inborn genetic diseases	Uncertain significance (Aug 01, 2022)
3-196654609-G-A		Inborn genetic diseases • Seizures, early-onset, with neurodegeneration and brain calcifications	Uncertain significance (Dec 13, 2023)
3-196659748-G-A		Seizures, early-onset, with neurodegeneration and brain calcifications	Uncertain significance (Jan 05, 2023)
3-196659777-G-A		Inborn genetic diseases	Uncertain significance (Dec 02, 2021)
3-196659804-G-A		Inborn genetic diseases	Likely benign (Jun 07, 2024)
3-196659817-C-A		Inborn genetic diseases	Uncertain significance (Dec 02, 2022)
3-196659822-G-A		Seizures, early-onset, with neurodegeneration and brain calcifications • Inborn genetic diseases	Conflicting classifications of pathogenicity (Aug 24, 2022)
3-196659828-T-C		Seizures, early-onset, with neurodegeneration and brain calcifications	Pathogenic (Oct 12, 2021)
3-196659830-AC-A		Seizures, early-onset, with neurodegeneration and brain calcifications	Pathogenic (May 15, 2020)
3-196659923-G-C		Inborn genetic diseases	Uncertain significance (Sep 12, 2023)
3-196659929-A-G		Inborn genetic diseases	Uncertain significance (Jan 24, 2023)
3-196659935-C-T		Inborn genetic diseases	Uncertain significance (Nov 15, 2021)
3-196659953-C-T		Seizures, early-onset, with neurodegeneration and brain calcifications	Pathogenic (Oct 12, 2021)
3-196659965-C-T		Inborn genetic diseases	Uncertain significance (Dec 21, 2023)
3-196660000-G-T		Inborn genetic diseases	Uncertain significance (Aug 12, 2021)
3-196660005-A-C		Inborn genetic diseases	Uncertain significance (Feb 15, 2023)
3-196660064-G-C		Inborn genetic diseases	Uncertain significance (Sep 13, 2023)
3-196660093-C-G		Seizures, early-onset, with neurodegeneration and brain calcifications	Benign (Sep 05, 2021)
3-196660094-C-A		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
3-196660187-C-A			Benign (May 14, 2018)
3-196660193-C-T		Inborn genetic diseases	Uncertain significance (Jul 11, 2023)
3-196660250-G-A		Inborn genetic diseases	Likely benign (Mar 07, 2024)
3-196660332-T-A		Inborn genetic diseases	Uncertain significance (Apr 15, 2024)
3-196660340-G-A		Inborn genetic diseases	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIGX	protein_coding	protein_coding	ENST00000296333	7	96233

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000238	0.759	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	92	129	0.713	0.00000650	1787
Missense in Polyphen		31	39.712	0.78063		516
Synonymous	0.939	38	46.1	0.824	0.00000230	546
Loss of Function	1.14	9	13.5	0.666	7.66e-7	174

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000293	0.000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000229	0.000229
Middle Eastern	0.000164	0.000163
South Asian	0.000262	0.000261
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential component of glycosylphosphatidylinositol- mannosyltransferase 1 which transfers the first of the 4 mannoses in the GPI-anchor precursors during GPI-anchor biosynthesis. Probably acts by stabilizing the mannosyltransferase PIGM (By similarity). {ECO:0000250}.
• 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: 0.0761

Intolerance Scores

• rvis_EVS: 0.5
• rvis_percentile_EVS: 79.89

Haploinsufficiency Scores

• pHI: 0.0233
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0795

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pigx

Gene ontology

• Biological process: GPI anchor biosynthetic process
• Cellular component: endoplasmic reticulum membrane;integral component of membrane