C10orf90

chromosome 10 open reading frame 90

Basic information

Region (hg38): 10:126424997-126798708

Links

ENSG00000154493NCBI:118611OMIM:617735HGNC:26563Uniprot:Q96M02AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C10orf90 gene.

  • not_provided (11 variants)
  • not_specified (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C10orf90 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001350921.2. 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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
5
missense
6
clinvar
1
clinvar
3
clinvar
10
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 6 1 9
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
C10orf90protein_codingprotein_codingENST00000284694 9245514
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
8.32e-150.06611256530951257480.000378
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.4484324071.060.00002324548
Missense in Polyphen103103.760.992631249
Synonymous0.5451561650.9460.00001001399
Loss of Function0.6922428.00.8590.00000135353

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006200.000620
Ashkenazi Jewish0.000.00
East Asian0.0003810.000381
Finnish0.00009240.0000924
European (Non-Finnish)0.0003230.000308
Middle Eastern0.0003810.000381
South Asian0.001020.00101
Other0.0003260.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Tumor suppressor that is required to sustain G2/M checkpoint after DNA damage. Mediates CDKN1A/p21 protein stability in a ubiquitin-independent manner (By similarity). May have a role in the assembly of primary cilia. {ECO:0000250}.;

Intolerance Scores

loftool
0.950
rvis_EVS
0.8
rvis_percentile_EVS
87.72

Haploinsufficiency Scores

pHI
0.0428
hipred
N
hipred_score
0.112
ghis
0.450

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
gene_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
D7Ertd443e
Phenotype
homeostasis/metabolism phenotype;

Gene ontology

Biological process
protein polyubiquitination;protein ubiquitination;regulation of centriole replication;protein stabilization
Cellular component
nucleoplasm;cytoplasm;centrosome;centriole;cytosol;plasma membrane;actin cytoskeleton
Molecular function
alpha-actinin binding;ubiquitin protein ligase activity