PAFAH2

platelet activating factor acetylhydrolase 2

Basic information

Region (hg38): 1:25959767-25998117

Links

ENSG00000158006 ∙ NCBI:5051 ∙ OMIM:602344 ∙ HGNC:8579 ∙ Uniprot:Q99487 ∙ 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 PAFAH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAFAH2 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						0
missense			34			34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	0	0

Variants in PAFAH2

This is a list of pathogenic ClinVar variants found in the PAFAH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-25962006-G-A		not specified	Uncertain significance (Aug 30, 2021)
1-25962021-G-A		not specified	Uncertain significance (Oct 23, 2024)
1-25962032-G-A		not specified	Uncertain significance (Sep 28, 2022)
1-25972579-C-T		not specified	Uncertain significance (Jan 06, 2023)
1-25972585-T-C		not specified	Uncertain significance (Jan 23, 2024)
1-25972591-G-A		not specified	Uncertain significance (Dec 28, 2023)
1-25972602-T-C		not specified	Uncertain significance (Jan 29, 2024)
1-25972614-T-C		not specified	Uncertain significance (Nov 07, 2023)
1-25972659-A-G		not specified	Uncertain significance (Jun 04, 2024)
1-25972701-T-C		not specified	Uncertain significance (Dec 02, 2024)
1-25974534-T-C		not specified	Uncertain significance (Apr 22, 2024)
1-25974562-C-G		not specified	Uncertain significance (Aug 01, 2024)
1-25974610-G-A		not specified	Uncertain significance (May 31, 2023)
1-25976688-T-G		not specified	Uncertain significance (Feb 08, 2025)
1-25982425-A-C		not specified	Uncertain significance (Sep 27, 2022)
1-25982426-C-T		not specified	Uncertain significance (May 14, 2024)
1-25982447-C-T		not specified	Uncertain significance (Aug 14, 2023)
1-25983957-G-A		not specified	Uncertain significance (Sep 09, 2024)
1-25983972-T-C		not specified	Uncertain significance (Sep 25, 2023)
1-25983981-C-G		not specified	Uncertain significance (Oct 29, 2024)
1-25984026-T-C		not specified	Uncertain significance (Jul 10, 2024)
1-25984055-T-C		not specified	Uncertain significance (May 20, 2024)
1-25984059-A-G		not specified	Uncertain significance (Jul 26, 2024)
1-25984083-G-A		not specified	Uncertain significance (May 24, 2024)
1-25984487-C-T		not specified	Uncertain significance (Apr 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAFAH2	protein_coding	protein_coding	ENST00000374282	10	38391

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.83e-9	0.558	125473	1	274	125748	0.00109

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.120	239	234	1.02	0.0000136	2559
Missense in Polyphen		90	85.112	1.0574		990
Synonymous	-0.255	88	85.0	1.04	0.00000457	765
Loss of Function	1.16	16	21.8	0.733	0.00000113	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00201	0.00201
Ashkenazi Jewish	0.00318	0.00318
East Asian	0.00347	0.00338
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000444	0.000440
Middle Eastern	0.00347	0.00338
South Asian	0.00261	0.00255
Other	0.000816	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has a marked selectivity for phospholipids with short acyl chains at the sn-2 position. May share a common physiologic function with the plasma-type enzyme. {ECO:0000269|PubMed:9494101}.
• Pathway: Ether lipid metabolism - Homo sapiens (human);Hemostasis;Platelet homeostasis (Consensus)

Intolerance Scores

• loftool: 0.935
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.73

Haploinsufficiency Scores

• pHI: 0.132
• hipred: N
• hipred_score: 0.144
• ghis: 0.445

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pafah2
• Phenotype: liver/biliary system phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: lipid metabolic process;blood coagulation;lipid catabolic process;negative regulation of apoptotic process
• Cellular component: endoplasmic reticulum membrane
• Molecular function: 1-alkyl-2-acetylglycerophosphocholine esterase activity;phospholipid binding