LFNG
Basic information
Region (hg38): 7:2512529-2529177
Links
Phenotypes
GenCC
Source:
- spondylocostal dysostosis 3, autosomal recessive (Definitive), mode of inheritance: AR
- spondylocostal dysostosis 3, autosomal recessive (Moderate), mode of inheritance: AR
- autosomal recessive spondylocostal dysostosis (Supportive), mode of inheritance: AR
- spondylocostal dysostosis 3, autosomal recessive (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Spondylocostal dysostosis 3, autosomal recessive | 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 | Musculoskeletal | 16385447; 20301771 |
ClinVar
This is a list of variants' phenotypes submitted to
- Spondylocostal_dysostosis_3,_autosomal_recessive (217 variants)
- Inborn_genetic_diseases (50 variants)
- not_provided (28 variants)
- LFNG-related_disorder (10 variants)
- not_specified (3 variants)
- Spondylocostal_dysostosis_2,_autosomal_recessive (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LFNG gene is commonly pathogenic or not. These statistics are base on transcript: NM_001040167.2. 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 | 78 | 82 | ||||
missense | 106 | 117 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 3 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
Total | 5 | 3 | 109 | 85 | 2 |
Highest pathogenic variant AF is 0.00000547629
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
LFNG | protein_coding | protein_coding | ENST00000222725 | 8 | 16649 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0976 | 0.895 | 125369 | 0 | 7 | 125376 | 0.0000279 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.616 | 172 | 196 | 0.876 | 0.0000140 | 2380 |
Missense in Polyphen | 38 | 77.38 | 0.49108 | 805 | ||
Synonymous | -1.32 | 105 | 89.1 | 1.18 | 0.00000694 | 829 |
Loss of Function | 2.36 | 4 | 13.3 | 0.302 | 5.75e-7 | 151 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000927 | 0.0000908 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000968 | 0.0000924 |
European (Non-Finnish) | 0.0000289 | 0.0000265 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Glycosyltransferase that initiates the elongation of O- linked fucose residues attached to EGF-like repeats in the extracellular domain of Notch molecules. Modulates NOTCH1 activity by modifying O-fucose residues at specific EGF-like domains resulting in inhibition of NOTCH1 activation by JAG1 and enhancement of NOTCH1 activation by DLL1 via an increase in its binding to DLL1 (By similarity). Decreases the binding of JAG1 to NOTCH2 but not that of DLL1 (PubMed:11346656). Essential mediator of somite segmentation and patterning (By similarity). {ECO:0000250|UniProtKB:O09010, ECO:0000269|PubMed:11346656}.;
- Disease
- DISEASE: Spondylocostal dysostosis 3, autosomal recessive (SCDO3) [MIM:609813]: A condition of variable severity associated with vertebral and rib segmentation defects. The main skeletal malformations include fusion of vertebrae, hemivertebrae, fusion of certain ribs, and other rib malformations. Deformity of the chest and spine (severe scoliosis, kyphoscoliosis and lordosis) is a natural consequence of the malformation and leads to a dwarf- like appearance. As the thorax is small, infants frequently have respiratory insufficiency and repeated respiratory infections resulting in life-threatening complications in the first year of life. {ECO:0000269|PubMed:16385447}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Other types of O-glycan biosynthesis - Homo sapiens (human);Notch signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);NOTCH-Ncore;Notch Signaling Pathway;Gene regulatory network modelling somitogenesis;Notch Signaling Pathway;Notch;Signal Transduction;segmentation clock;Notch;Pre-NOTCH Processing in Golgi;Pre-NOTCH Expression and Processing;Signaling by NOTCH
(Consensus)
Recessive Scores
- pRec
- 0.189
Intolerance Scores
- loftool
- 0.907
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 50.34
Haploinsufficiency Scores
- pHI
- 0.270
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.515
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.685
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lfng
- 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); hearing/vestibular/ear phenotype; vision/eye phenotype; skeleton phenotype; embryo phenotype; respiratory system 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; 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); hematopoietic system phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- lfng
- Affected structure
- CiD
- Phenotype tag
- abnormal
- Phenotype quality
- increased amount
Gene ontology
- Biological process
- ovarian follicle development;somitogenesis;marginal zone B cell differentiation;compartment pattern specification;regulation of Notch signaling pathway;animal organ morphogenesis;regulation of somitogenesis;T cell differentiation;positive regulation of protein binding;protein O-linked fucosylation;positive regulation of Notch signaling pathway;positive regulation of meiotic cell cycle;negative regulation of Notch signaling pathway involved in somitogenesis
- Cellular component
- extracellular region;integral component of Golgi membrane;extracellular vesicle
- Molecular function
- molecular_function;acetylglucosaminyltransferase activity;O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity;metal ion binding