PIGF

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

Basic information

Region (hg38): 2:46580937-46617055

Links

ENSG00000151665 ∙ NCBI:5281 ∙ OMIM:600153 ∙ HGNC:8962 ∙ Uniprot:Q07326 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	33386993

ClinVar

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

• Short stature with microcephaly and distinctive facies (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIGF 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			15		1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region	1					1
non coding			3		1	4
Total	0	0	18	1	2

Variants in PIGF

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

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

Position	Type	Phenotype	Significance	ClinVar
2-46580947-T-C		not specified	Uncertain significance (Aug 16, 2021)
2-46581025-A-G		not specified	Uncertain significance (Jun 29, 2022)
2-46581028-A-T		not specified	Uncertain significance (Dec 12, 2023)
2-46581079-C-T		not specified	Uncertain significance (Apr 12, 2024)
2-46581482-T-C		not specified	Uncertain significance (Dec 08, 2023)
2-46581484-G-T		not specified	Uncertain significance (Sep 01, 2021)
2-46581519-T-A		not specified	Uncertain significance (May 17, 2023)
2-46581520-C-A		not specified	Uncertain significance (May 17, 2023)
2-46581549-C-T		not specified	Uncertain significance (Aug 16, 2022)
2-46592506-G-C		Onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome	Pathogenic (Jun 07, 2021)
2-46592537-T-C		not specified	Uncertain significance (Nov 22, 2023)
2-46592543-T-C		not specified	Uncertain significance (Apr 11, 2023)
2-46612250-G-A		PIGF-related condition	Likely benign (Jul 10, 2024)
2-46612316-C-A		not specified	Uncertain significance (Apr 10, 2023)
2-46612348-G-GA		PIGF-related condition	Likely benign (May 24, 2024)
2-46613761-T-C		not specified	Uncertain significance (Jun 29, 2023)
2-46613765-G-C		not specified	Uncertain significance (Feb 28, 2023)
2-46613782-T-C		not specified	Uncertain significance (Jun 22, 2024)
2-46614938-T-A		not specified	Uncertain significance (Jun 18, 2021)
2-46614941-T-C		PIGF-related condition	Likely benign (Apr 02, 2024)
2-46614973-T-C			Likely benign (Dec 01, 2021)
2-46614975-G-T		not specified	Uncertain significance (Aug 13, 2021)
2-46614980-A-G			Benign (Aug 01, 2024)
2-46614999-G-C		not specified	Uncertain significance (Sep 17, 2021)
2-46615002-T-G		not specified	Uncertain significance (Apr 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIGF	protein_coding	protein_coding	ENST00000281382	5	36183

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000720	0.772	125696	0	27	125723	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.555	115	99.4	1.16	0.00000455	1382
Missense in Polyphen		33	29.39	1.1228		414
Synonymous	-0.0485	39	38.6	1.01	0.00000200	424
Loss of Function	1.02	6	9.35	0.642	3.93e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000447	0.000447
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000970	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in GPI-anchor biosynthesis through the transfer of ethanolamine phosphate to the third mannose of GPI. {ECO:0000250}.
• Pathway: Glycosylphosphatidylinositol (GPI)-anchor biosynthesis - Homo sapiens (human);VEGF Signaling Pathway;Exercise-induced Circadian Regulation;Synthesis of glycosylphosphatidylinositol (GPI);Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins;Phosphatidylinositol phosphate metabolism (Consensus)

Recessive Scores

• pRec: 0.148

Intolerance Scores

• loftool: 0.250
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.27

Haploinsufficiency Scores

• pHI: 0.647
• hipred: N
• hipred_score: 0.216
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0482

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pigf
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); skeleton phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: GPI anchor biosynthetic process;preassembly of GPI anchor in ER membrane
• Cellular component: endoplasmic reticulum membrane;integral component of membrane
• Molecular function: ethanolaminephosphotransferase activity