C9orf43

chromosome 9 open reading frame 43

Basic information

Region (hg38): 9:113410054-113429690

Links

ENSG00000157653NCBI:257169HGNC:23570Uniprot:Q8TAL5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C9orf43 gene.

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
2
clinvar
1
clinvar
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)2354312
9-113410128-C-T not specified Uncertain significance (Aug 16, 2022)2307428
9-113410136-G-A not specified Uncertain significance (Sep 22, 2021)2219726
9-113419113-C-T not specified Uncertain significance (Sep 27, 2021)2252033
9-113422578-C-T not specified Likely benign (Oct 06, 2021)2376280
9-113423398-G-A not specified Uncertain significance (Nov 08, 2021)2259052

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
C9orf43protein_codingprotein_codingENST00000288462 1319631
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.36e-110.552108149808167901257470.0726
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1722432510.9690.00001303035
Missense in Polyphen5058.7590.85093741
Synonymous-0.76310494.61.100.00000544845
Loss of Function1.332027.50.7260.00000150307

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.05160.0515
Ashkenazi Jewish0.05690.0566
East Asian0.04830.0480
Finnish0.1180.119
European (Non-Finnish)0.08910.0888
Middle Eastern0.04830.0480
South Asian0.07560.0743
Other0.07000.0699

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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