PAFAH1B3

platelet activating factor acetylhydrolase 1b catalytic subunit 3

Basic information

Region (hg38): 19:42297033-42303546

Links

ENSG00000079462 ∙ NCBI:5050 ∙ OMIM:603074 ∙ HGNC:8576 ∙ Uniprot:Q15102 ∙ 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 PAFAH1B3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAFAH1B3 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	18	1	0

Variants in PAFAH1B3

This is a list of pathogenic ClinVar variants found in the PAFAH1B3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-42297134-G-A		not specified	Uncertain significance (Feb 10, 2025)
19-42297155-C-G		not specified	Uncertain significance (Jul 27, 2022)
19-42297157-C-T		not specified	Uncertain significance (Feb 28, 2024)
19-42297158-G-A		not specified	Uncertain significance (Mar 14, 2023)
19-42297203-A-G		Autism spectrum disorder	association (-)
19-42297251-C-T		not specified	Uncertain significance (Dec 02, 2021)
19-42297295-C-T		not specified	Uncertain significance (Mar 15, 2024)
19-42297305-C-T		not specified	Uncertain significance (Apr 20, 2023)
19-42297316-C-T		not specified	Likely benign (Nov 06, 2024)
19-42297325-T-A		not specified	Uncertain significance (Jan 23, 2025)
19-42297326-C-T		not specified	Uncertain significance (Jul 12, 2023)
19-42297328-C-T		not specified	Uncertain significance (May 14, 2024)
19-42299989-T-C		not specified	Uncertain significance (Nov 09, 2021)
19-42300005-T-A		not specified	Uncertain significance (Jan 03, 2024)
19-42300043-T-C		not specified	Uncertain significance (Oct 20, 2023)
19-42300165-G-A			Likely benign (May 20, 2018)
19-42300179-G-A		not specified	Uncertain significance (Jan 04, 2022)
19-42300214-A-G		not specified	Uncertain significance (Mar 01, 2024)
19-42300224-G-C		not specified	Uncertain significance (Jul 06, 2021)
19-42300278-C-T		not specified	Uncertain significance (Feb 24, 2025)
19-42300281-G-A		not specified	Uncertain significance (Nov 21, 2022)
19-42301952-C-T		not specified	Uncertain significance (May 16, 2022)
19-42302255-C-T		not specified	Uncertain significance (Sep 11, 2024)
19-42302280-C-G		not specified	Uncertain significance (Nov 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAFAH1B3	protein_coding	protein_coding	ENST00000538771	5	6514

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00248	0.936	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	112	148	0.755	0.00000889	1473
Missense in Polyphen		28	43.116	0.64941		470
Synonymous	0.166	59	60.6	0.973	0.00000339	494
Loss of Function	1.63	6	12.1	0.494	7.76e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000911	0.0000879
Middle Eastern	0.000163	0.000163
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. Plays an important role during the development of brain.
• Pathway: Ether lipid metabolism - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;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: 0.145

Intolerance Scores

• loftool: 0.531
• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.490
• hipred: N
• hipred_score: 0.393
• ghis: 0.628

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pafah1b3
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; normal phenotype; reproductive system phenotype

Gene ontology

• Biological process: lipid metabolic process;spermatogenesis;nervous system development;brain development;lipid catabolic process
• Cellular component: cytoplasm;cytosol;membrane
• Molecular function: 1-alkyl-2-acetylglycerophosphocholine esterase activity;phospholipase A2 activity;protein binding;identical protein binding;protein heterodimerization activity;platelet-activating factor acetyltransferase activity