PORCN
Basic information
Region (hg38): X:48508959-48520814
Previous symbols: [ "DHOF" ]
Links
Phenotypes
GenCC
Source:
- focal dermal hypoplasia (Strong), mode of inheritance: XL
- focal dermal hypoplasia (Definitive), mode of inheritance: XL
- focal dermal hypoplasia (Supportive), mode of inheritance: XL
- microphthalmia, isolated, with coloboma (Supportive), mode of inheritance: AD
- focal dermal hypoplasia (Definitive), mode of inheritance: XL
- focal dermal hypoplasia (Definitive), mode of inheritance: XL
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Focal dermal hypoplasia | XL | 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 | Audiologic/Otolaryngologic; Craniofacial; Dental; Dermatologic; Musculoskeletal; Neurologic; Ophthalmologic | 13948891; 1190805; 843447; 17546031; 17546030; 18325042; 19309688; 19863546; 19586929; 20420028; 21332693; 21472892; 21484999; 21732017; 22414489; 22250236; 22735390; 23131169; 23399492 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (116 variants)
- Focal_dermal_hypoplasia (44 variants)
- Inborn_genetic_diseases (36 variants)
- PORCN-related_disorder (12 variants)
- not_specified (5 variants)
- History_of_neurodevelopmental_disorder (1 variants)
- Genetic_developmental_and_epileptic_encephalopathy (1 variants)
- Anophthalmia-microphthalmia_syndrome (1 variants)
- Global_developmental_delay (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PORCN gene is commonly pathogenic or not. These statistics are base on transcript: NM_000203475.3. 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 | 19 | 30 | ||||
missense | 13 | 63 | 16 | 98 | ||
nonsense | 14 | 16 | ||||
start loss | 1 | 1 | ||||
frameshift | 10 | 15 | ||||
splice donor/acceptor (+/-2bp) | 11 | |||||
Total | 35 | 26 | 65 | 35 | 10 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PORCN | protein_coding | protein_coding | ENST00000326194 | 14 | 11853 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 0.000468 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.37 | 112 | 208 | 0.538 | 0.0000186 | 2975 |
Missense in Polyphen | 28 | 74.771 | 0.37448 | 1087 | ||
Synonymous | 2.27 | 61 | 88.2 | 0.692 | 0.00000798 | 953 |
Loss of Function | 4.35 | 0 | 22.1 | 0.00 | 0.00000175 | 293 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Protein-serine O-palmitoleoyltransferase that acts as a key regulator of the Wnt signaling pathway by mediating the attachment of palmitoleate, a 16-carbon monounsaturated fatty acid (C16:1), to Wnt proteins. Serine palmitoleylation of WNT proteins is required for efficient binding to frizzled receptors. {ECO:0000250|UniProtKB:Q9JJJ7, ECO:0000269|PubMed:12034504, ECO:0000269|PubMed:20826466, ECO:0000269|PubMed:24292069}.;
- Pathway
- Wnt signaling pathway - Homo sapiens (human);Wnt Signaling Pathway;Disease;Signaling by WNT;Signal Transduction;WNT ligand biogenesis and trafficking;WNT ligand secretion is abrogated by the PORCN inhibitor LGK974;Signaling by WNT in cancer;Diseases of signal transduction
(Consensus)
Recessive Scores
- pRec
- 0.290
Intolerance Scores
- loftool
- rvis_EVS
- -0.52
- rvis_percentile_EVS
- 21.2
Haploinsufficiency Scores
- pHI
- 0.303
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.478
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.238
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Porcn
- Phenotype
- normal phenotype; 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); reproductive system phenotype; embryo phenotype; renal/urinary system phenotype; skeleton phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); craniofacial 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- porcn
- Affected structure
- neural tube
- Phenotype tag
- abnormal
- Phenotype quality
- shortened
Gene ontology
- Biological process
- protein lipidation;glycoprotein metabolic process;Wnt signaling pathway;protein palmitoleylation;canonical Wnt signaling pathway;regulation of postsynaptic membrane neurotransmitter receptor levels
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;integral component of endoplasmic reticulum membrane;AMPA glutamate receptor complex;glutamatergic synapse
- Molecular function
- Wnt-protein binding;palmitoleoyltransferase activity