PNPLA7

patatin like phospholipase domain containing 7, the group of Patatin like phospholipase domain containing

Basic information

Region (hg38): 9:137459952-137550402

Previous symbols: [ "C9orf111" ]

Links

ENSG00000130653 ∙ NCBI:375775 ∙ OMIM:612122 ∙ HGNC:24768 ∙ Uniprot:Q6ZV29 ∙ 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 PNPLA7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PNPLA7 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				6	1	7
missense			163	17	1	181
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	163	23	3

Variants in PNPLA7

This is a list of pathogenic ClinVar variants found in the PNPLA7 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-137460421-G-C		not specified	Uncertain significance (Apr 14, 2022)
9-137460445-G-C		PNPLA7-related condition	Uncertain significance (Sep 04, 2024)
9-137460463-G-A		not specified	Likely benign (Nov 10, 2024)
9-137460635-A-G		not specified	Likely benign (Nov 23, 2024)
9-137460711-C-T		not specified	Uncertain significance (Jul 16, 2024)
9-137460719-G-A		not specified	Uncertain significance (Jul 06, 2024)
9-137460719-G-T		not specified	Uncertain significance (Dec 09, 2023)
9-137461603-G-C		not specified	Uncertain significance (Jul 14, 2022)
9-137461990-C-T		not specified	Uncertain significance (Dec 28, 2023)
9-137461995-C-T		not specified	Uncertain significance (Aug 02, 2021)
9-137461999-C-T		not specified	Uncertain significance (Nov 15, 2024)
9-137462004-A-G		Premature ovarian failure	Uncertain significance (Apr 22, 2019)
9-137462185-C-A		not specified	Uncertain significance (Mar 23, 2023)
9-137462199-C-T		not specified	Likely benign (Dec 19, 2022)
9-137462284-G-A			Likely benign (Apr 01, 2022)
9-137462690-C-T		not specified	Uncertain significance (Mar 08, 2024)
9-137462705-G-T		not specified	Uncertain significance (Feb 06, 2024)
9-137462734-C-T		Peripheral neuropathy, autosomal recessive, with or without impaired intellectual development • not specified	Uncertain significance (Aug 07, 2024)
9-137462735-C-T		not specified	Uncertain significance (Sep 05, 2024)
9-137462743-G-A		not specified	Uncertain significance (Jul 22, 2024)
9-137462749-C-G		not specified	Uncertain significance (Apr 04, 2024)
9-137462750-C-G		not specified	Uncertain significance (Nov 15, 2024)
9-137462752-T-C		not specified	Uncertain significance (Oct 05, 2023)
9-137462767-G-A		not specified	Uncertain significance (May 24, 2023)
9-137462776-C-T		not specified	Likely benign (May 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PNPLA7	protein_coding	protein_coding	ENST00000406427	35	90583

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.37e-37	0.000196	121932	16	3799	125747	0.0153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.690	801	858	0.934	0.0000586	8580
Missense in Polyphen		309	347.3	0.88973		3639
Synonymous	-0.542	390	377	1.04	0.0000281	2747
Loss of Function	1.00	61	70.0	0.871	0.00000357	771

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0298	0.0277
Ashkenazi Jewish	0.0203	0.0202
East Asian	0.00178	0.00174
Finnish	0.0130	0.0121
European (Non-Finnish)	0.0237	0.0225
Middle Eastern	0.00178	0.00174
South Asian	0.00459	0.00432
Other	0.0149	0.0144

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine hydrolase, whose specific chemical modification by certain organophosphorus (OP) compounds leads to distal axonopathy. {ECO:0000250}.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Metabolism of lipids;Metabolism;Glycerophospholipid catabolism;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.0978

Intolerance Scores

• loftool: 0.230
• rvis_EVS: 0.16
• rvis_percentile_EVS: 64.97

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.197
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.359

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pnpla7

Gene ontology

• Biological process: lipid catabolic process
• Cellular component: lysosomal membrane;endoplasmic reticulum;integral component of membrane;nuclear membrane;mitochondrial membrane
• Molecular function: lysophospholipase activity