NSFL1C
Basic information
Region (hg38): 20:1442162-1473842
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (36 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NSFL1C gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016143.5. 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 | 1 | |||||
| missense | 36 | 37 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 36 | 1 | 1 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NSFL1C | protein_coding | protein_coding | ENST00000476071 | 10 | 31681 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0495 | 0.950 | 125728 | 0 | 18 | 125746 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.46 | 154 | 214 | 0.719 | 0.0000119 | 2430 |
| Missense in Polyphen | 53 | 87.071 | 0.6087 | 981 | ||
| Synonymous | -0.139 | 87 | 85.4 | 1.02 | 0.00000511 | 724 |
| Loss of Function | 2.92 | 6 | 20.1 | 0.298 | 0.00000102 | 225 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000905 | 0.0000905 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000296 | 0.000294 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Reduces the ATPase activity of VCP (By similarity). Necessary for the fragmentation of Golgi stacks during mitosis and for VCP-mediated reassembly of Golgi stacks after mitosis (By similarity). May play a role in VCP-mediated formation of transitional endoplasmic reticulum (tER) (By similarity). Inhibits the activity of CTSL (in vitro) (PubMed:15498563). Together with UBXN2B/p37, regulates the centrosomal levels of kinase AURKA/Aurora A during mitotic progression by promoting AURKA removal from centrosomes in prophase (PubMed:23649807). Also, regulates spindle orientation during mitosis (PubMed:23649807). {ECO:0000250|UniProtKB:O35987, ECO:0000269|PubMed:15498563, ECO:0000269|PubMed:23649807}.;
- Pathway
- Protein processing in endoplasmic reticulum - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.132
Intolerance Scores
- loftool
- 0.731
- rvis_EVS
- -0.2
- rvis_percentile_EVS
- 38.82
Haploinsufficiency Scores
- pHI
- 0.184
- hipred
- Y
- hipred_score
- 0.745
- ghis
- 0.558
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.820
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | High | Medium | High |
Mouse Genome Informatics
- Gene name
- Nsfl1c
- Phenotype
Gene ontology
- Biological process
- autophagosome assembly;establishment of mitotic spindle orientation;Golgi organization;nuclear envelope reassembly;proteasome-mediated ubiquitin-dependent protein catabolic process;positive regulation of mitotic centrosome separation;membrane fusion;negative regulation of protein localization to centrosome
- Cellular component
- nucleoplasm;chromosome;Golgi stack;cytosol;plasma membrane;spindle pole centrosome;intermediate filament cytoskeleton;VCP-NSFL1C complex
- Molecular function
- protein binding;phospholipid binding;ubiquitin binding;ATPase binding