PAFAH1B2

platelet activating factor acetylhydrolase 1b catalytic subunit 2

Basic information

Region (hg38): 11:117144284-117176894

Links

ENSG00000168092 ∙ NCBI:5049 ∙ OMIM:602508 ∙ HGNC:8575 ∙ Uniprot:P68402 ∙ 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 PAFAH1B2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAFAH1B2 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			3	1		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	1

Variants in PAFAH1B2

This is a list of pathogenic ClinVar variants found in the PAFAH1B2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-117152483-G-T			Benign (Jan 11, 2018)
11-117167515-A-G		not specified	Uncertain significance (Aug 11, 2024)
11-117167538-G-A		not specified	Uncertain significance (Jun 03, 2022)
11-117167554-C-T		not specified	Uncertain significance (Aug 04, 2023)
11-117171692-C-T			Likely benign (Nov 01, 2023)
11-117171707-C-G		not specified	Uncertain significance (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAFAH1B2	protein_coding	protein_coding	ENST00000527958	5	32628

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.934	0.0659	125705	0	1	125706	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	76	129	0.591	0.00000667	1505
Missense in Polyphen		14	44.861	0.31208		525
Synonymous	0.0345	50	50.3	0.994	0.00000327	437
Loss of Function	3.09	1	13.0	0.0766	7.85e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inactivates PAF by removing the acetyl group at the sn-2 position. This is a catalytic subunit.
• Pathway: Ether lipid metabolism - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Neutrophil degranulation;Vesicle-mediated transport;Membrane Trafficking;Innate Immune System;Immune System;COPI-independent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Lissencephaly gene (LIS1) in neuronal migration and development;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.0777
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.659
• hipred: Y
• hipred_score: 0.749
• ghis: 0.632

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pafah1b2
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: lipid metabolic process;spermatogenesis;brain development;lipid catabolic process;positive regulation of macroautophagy;neutrophil degranulation
• Cellular component: fibrillar center;extracellular region;nucleolus;cytoplasm;cytosol;plasma membrane;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
• Molecular function: 1-alkyl-2-acetylglycerophosphocholine esterase activity;phospholipase A2 activity;protein binding;protein homodimerization activity;protein heterodimerization activity;platelet-activating factor acetyltransferase activity