C10orf90

chromosome 10 open reading frame 90

Basic information

Region (hg38): 10:126424996-126798708

Links

ENSG00000154493 ∙ NCBI:118611 ∙ OMIM:617735 ∙ HGNC:26563 ∙ Uniprot:Q96M02 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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)
• Inborn genetic diseases (5 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.

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					5	5
missense			5	1	3	9
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	5	1	9

Variants in C10orf90

This is a list of pathogenic ClinVar variants found in the C10orf90 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-126425986-A-G			Benign (Aug 02, 2017)
10-126459169-G-A			Benign (Feb 25, 2018)
10-126459180-C-T			Benign (Jun 29, 2018)
10-126459213-G-A		not specified	Uncertain significance (Jul 09, 2021)
10-126461480-C-A		not specified	Uncertain significance (Sep 01, 2021)
10-126461491-C-A			Benign (Jul 13, 2018)
10-126464816-G-A			Benign (Dec 31, 2019)
10-126464859-G-A			Benign (Dec 31, 2019)
10-126504015-G-A			Benign (Dec 31, 2019)
10-126504024-A-T			Benign (Jun 29, 2018)
10-126504092-T-C		not specified	Uncertain significance (Sep 28, 2021)
10-126504340-C-T		not specified	Uncertain significance (Aug 02, 2021)
10-126504439-A-G		not specified	Uncertain significance (Aug 30, 2021)
10-126504556-C-T			Likely benign (Dec 31, 2019)
10-126504743-C-T			Benign (Dec 31, 2019)
10-126504880-A-G		not specified	Uncertain significance (Oct 26, 2021)
10-126505010-T-G			Benign (Jul 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C10orf90	protein_coding	protein_coding	ENST00000284694	9	245514

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.32e-15	0.0661	125653	0	95	125748	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.448	432	407	1.06	0.0000232	4548
Missense in Polyphen		103	103.76	0.99263		1249
Synonymous	0.545	156	165	0.946	0.0000100	1399
Loss of Function	0.692	24	28.0	0.859	0.00000135	353

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000620	0.000620
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000323	0.000308
Middle Eastern	0.000381	0.000381
South Asian	0.00102	0.00101
Other	0.000326	0.000326

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

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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