PNPLA1
Basic information
Region (hg38): 6:36243203-36313955
Links
Phenotypes
GenCC
Source:
- autosomal recessive congenital ichthyosis 10 (Strong), mode of inheritance: AR
- autosomal recessive congenital ichthyosis 10 (Moderate), mode of inheritance: AR
- autosomal recessive congenital ichthyosis 10 (Strong), mode of inheritance: AR
- autosomal recessive congenital ichthyosis 10 (Strong), mode of inheritance: AR
- congenital non-bullous ichthyosiform erythroderma (Supportive), mode of inheritance: AR
- autosomal recessive congenital ichthyosis 10 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Ichthyosis, congenital, autosomal recessive 10 | 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 | Dermatologic | 22246504; 24344921; 26691440; 28403545 |
ClinVar
This is a list of variants' phenotypes submitted to
- Autosomal_recessive_congenital_ichthyosis_10 (96 variants)
- Inborn_genetic_diseases (71 variants)
- not_provided (61 variants)
- Congenital_ichthyosiform_erythroderma (19 variants)
- Lamellar_ichthyosis (10 variants)
- not_specified (9 variants)
- PNPLA1-related_disorder (8 variants)
- EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
- Autosomal_recessive_congenital_ichthyosis (1 variants)
- Abnormality_of_the_skin (1 variants)
- Ichthyosis (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PNPLA1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001374623.1. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 16 | 25 | ||||
missense | 21 | 92 | 12 | 139 | ||
nonsense | 7 | |||||
start loss | 0 | |||||
frameshift | 10 | |||||
splice donor/acceptor (+/-2bp) | 4 | |||||
Total | 15 | 32 | 102 | 29 | 7 |
Highest pathogenic variant AF is 0.0000412602
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PNPLA1 | protein_coding | protein_coding | ENST00000394571 | 8 | 65393 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000185 | 0.995 | 125719 | 0 | 29 | 125748 | 0.000115 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.734 | 283 | 320 | 0.884 | 0.0000189 | 3395 |
Missense in Polyphen | 88 | 114.93 | 0.76565 | 1123 | ||
Synonymous | -0.815 | 153 | 141 | 1.09 | 0.00000947 | 1142 |
Loss of Function | 2.47 | 10 | 22.7 | 0.441 | 0.00000130 | 237 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000370 | 0.000369 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000167 | 0.000167 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000653 | 0.0000653 |
Other | 0.000333 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Lipid hydrolase. Important in the formation of the epidermal lipid barrier. Plays a role in glycerophospholipid metabolism. {ECO:0000269|PubMed:22246504}.;
Intolerance Scores
- loftool
- 0.745
- rvis_EVS
- 1.27
- rvis_percentile_EVS
- 93.63
Haploinsufficiency Scores
- pHI
- 0.132
- hipred
- N
- hipred_score
- 0.210
- ghis
- 0.407
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0685
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pnpla1
- Phenotype
- homeostasis/metabolism phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); limbs/digits/tail phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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);
Gene ontology
- Biological process
- triglyceride catabolic process;lipid homeostasis
- Cellular component
- cytoplasm;lipid droplet;membrane
- Molecular function
- triglyceride lipase activity