SFTPC
Basic information
Region (hg38): 8:22156913-22164479
Previous symbols: [ "SFTP2" ]
Links
Phenotypes
GenCC
Source:
- surfactant metabolism dysfunction, pulmonary, 2 (Strong), mode of inheritance: AD
- surfactant metabolism dysfunction, pulmonary, 2 (Definitive), mode of inheritance: AD
- chronic respiratory distress with surfactant metabolism deficiency (Supportive), mode of inheritance: AD
- SFTPC- related interstitial lung disease (Supportive), mode of inheritance: AD
- surfactant metabolism dysfunction, pulmonary, 2 (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Surfactant metabolism dysfunction, pulmonary, 2 | AD | Pulmonary | There have been reports of individuals who received benefit from medical treatment, including hydroxychloroquine, whole-lung lavage, systemic corticosteroids, azathioprine; Lung transplantation may be indicated in individuals with severe and/or refractory disease | Pulmonary | 11207353; 11445799; 11893657; 11991887; 15039969; 15293602; 15647591; 19443464 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (77 variants)
- Hereditary_pulmonary_alveolar_proteinosis (66 variants)
- Surfactant_metabolism_dysfunction,_pulmonary,_2 (48 variants)
- Interstitial_lung_disease_2 (25 variants)
- SFTPC-related_disorder (11 variants)
- not_specified (8 variants)
- Pulmonary_fibrosis (5 variants)
- Pulmonary_Surfactant_Metabolism_Dysfunction,_Dominant (3 variants)
- Surfactant_metabolism_dysfunction,_pulmonary,_1 (1 variants)
- Inborn_genetic_diseases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFTPC gene is commonly pathogenic or not. These statistics are base on transcript: NM_001317778.2. 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 | 24 | ||||
missense | 12 | 66 | 10 | 96 | ||
nonsense | 3 | |||||
start loss | 0 | |||||
frameshift | 7 | |||||
splice donor/acceptor (+/-2bp) | 5 | |||||
Total | 13 | 18 | 72 | 29 | 3 |
Highest pathogenic variant AF is 0.00000309874
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SFTPC | protein_coding | protein_coding | ENST00000318561 | 5 | 7567 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000753 | 0.781 | 124781 | 0 | 16 | 124797 | 0.0000641 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.849 | 90 | 116 | 0.778 | 0.00000713 | 1254 |
Missense in Polyphen | 26 | 45.123 | 0.5762 | 523 | ||
Synonymous | -1.02 | 57 | 48.0 | 1.19 | 0.00000311 | 420 |
Loss of Function | 1.04 | 6 | 9.44 | 0.636 | 5.40e-7 | 102 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000290 | 0.0000290 |
Ashkenazi Jewish | 0.0000993 | 0.0000993 |
East Asian | 0.000167 | 0.000167 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000354 | 0.0000353 |
Middle Eastern | 0.000167 | 0.000167 |
South Asian | 0.000197 | 0.000196 |
Other | 0.000165 | 0.000165 |
dbNSFP
Source:
- Function
- FUNCTION: Pulmonary surfactant associated proteins promote alveolar stability by lowering the surface tension at the air- liquid interface in the peripheral air spaces.;
- Disease
- DISEASE: Pulmonary surfactant metabolism dysfunction 2 (SMDP2) [MIM:610913]: A rare disease associated with progressive respiratory insufficiency and lung disease with a variable clinical course, due to impaired surfactant homeostasis. It is characterized by alveolar filling with floccular material that stains positive using the periodic acid-Schiff method and is derived from surfactant phospholipids and protein components. Excessive lipoproteins accumulation in the alveoli results in severe respiratory distress. {ECO:0000269|PubMed:11991887, ECO:0000269|PubMed:15039969, ECO:0000269|PubMed:15293602, ECO:0000269|PubMed:15557112, ECO:0000269|PubMed:15572558}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Respiratory distress syndrome in premature infants (RDS) [MIM:267450]: A lung disease affecting usually premature newborn infants. It is characterized by deficient gas exchange, diffuse atelectasis, high-permeability lung edema and fibrin-rich alveolar deposits called 'hyaline membranes'. {ECO:0000269|PubMed:14735158}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.;
- Pathway
- Surfactant metabolism;Lung fibrosis;Surfactant metabolism;Metabolism of proteins
(Consensus)
Recessive Scores
- pRec
- 0.234
Intolerance Scores
- loftool
- 0.122
- rvis_EVS
- 0.22
- rvis_percentile_EVS
- 68.13
Haploinsufficiency Scores
- pHI
- 0.257
- hipred
- N
- hipred_score
- 0.290
- ghis
- 0.415
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.516
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | High | Medium | High |
Mouse Genome Informatics
- Gene name
- Sftpc
- Phenotype
- cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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); reproductive system phenotype; neoplasm; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; immune system phenotype; vision/eye phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- respiratory gaseous exchange;cellular protein metabolic process
- Cellular component
- extracellular region;extracellular space;endoplasmic reticulum membrane;lamellar body;clathrin-coated endocytic vesicle;multivesicular body lumen
- Molecular function
- protein binding;identical protein binding