C10orf120

chromosome 10 open reading frame 120

Basic information

Region (hg38): 10:122697709-122699846

Links

ENSG00000183559

∙ NCBI:399814 ∙ ∙ HGNC:25707 ∙ Uniprot:Q5SQS8 ∙ 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 C10orf120 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C10orf120 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 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	3	0	0

Variants in C10orf120

This is a list of pathogenic ClinVar variants found in the C10orf120 region.

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

Position	Phenotype	Significance	ClinVar
10-122697891-G-C	not specified	Uncertain significance (Sep 01, 2021)	2393623
10-122698170-G-A	not specified	Uncertain significance (Aug 11, 2021)	3135655
10-122699637-G-C	not specified	Uncertain significance (Oct 20, 2024)	2205674

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C10orf120	protein_coding	protein_coding	ENST00000329446	3	2114

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000355	0.218	125674	0	15	125689	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.234	202	193	1.05	0.0000108	2213
Missense in Polyphen		51	50.716	1.0056		605
Synonymous	1.21	53	65.5	0.809	0.00000340	613
Loss of Function	-0.561	6	4.69	1.28	1.98e-7	57

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000762	0.000761
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000762	0.000761
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

loftool: 0.953
rvis_EVS: 0.11
rvis_percentile_EVS: 62

Haploinsufficiency Scores

pHI: 0.0570
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: 4933402N03Rik
Phenotype: homeostasis/metabolism phenotype; craniofacial phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); skeleton phenotype;