C9orf43
Basic information
Region (hg38): 9:113410054-113429690
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the C9orf43 gene is commonly pathogenic or not.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 3 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 2 | 1 | 0 |
Variants in C9orf43
This is a list of pathogenic ClinVar variants found in the C9orf43 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
9-113410107-G-A | not specified | Uncertain significance (Jun 30, 2022) | ||
9-113410128-C-T | not specified | Uncertain significance (Aug 16, 2022) | ||
9-113410136-G-A | not specified | Uncertain significance (Sep 22, 2021) | ||
9-113419113-C-T | not specified | Uncertain significance (Sep 27, 2021) | ||
9-113422578-C-T | not specified | Likely benign (Oct 06, 2021) | ||
9-113423398-G-A | not specified | Uncertain significance (Nov 08, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
C9orf43 | protein_coding | protein_coding | ENST00000288462 | 13 | 19631 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
4.36e-11 | 0.552 | 108149 | 808 | 16790 | 125747 | 0.0726 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.172 | 243 | 251 | 0.969 | 0.0000130 | 3035 |
Missense in Polyphen | 50 | 58.759 | 0.85093 | 741 | ||
Synonymous | -0.763 | 104 | 94.6 | 1.10 | 0.00000544 | 845 |
Loss of Function | 1.33 | 20 | 27.5 | 0.726 | 0.00000150 | 307 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0516 | 0.0515 |
Ashkenazi Jewish | 0.0569 | 0.0566 |
East Asian | 0.0483 | 0.0480 |
Finnish | 0.118 | 0.119 |
European (Non-Finnish) | 0.0891 | 0.0888 |
Middle Eastern | 0.0483 | 0.0480 |
South Asian | 0.0756 | 0.0743 |
Other | 0.0700 | 0.0699 |
dbNSFP
Source:
Intolerance Scores
- loftool
- 0.915
- rvis_EVS
- 1.44
- rvis_percentile_EVS
- 95.08
Haploinsufficiency Scores
- pHI
- 0.0257
- hipred
- N
- hipred_score
- 0.123
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- gene_indispensability_score
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- 4933430I17Rik
- Phenotype
- skeleton phenotype; limbs/digits/tail phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- Cellular component
- Molecular function
- protein binding