C10orf55

chromosome 10 putative open reading frame 55

Basic information

Region (hg38): 10:73908103-73922810

Links

ENSG00000222047 ∙ NCBI:414236 ∙ ∙ HGNC:31008 ∙ Uniprot:Q5SWW7 ∙ 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 C10orf55 gene.

• Quebec platelet disorder (69 variants)
• not provided (20 variants)
• Inborn genetic diseases (13 variants)
• Alzheimer disease, late-onset, susceptibility to (1 variants)
• PLAU-related condition (1 variants)
• Hirschsprung disease, susceptibility to, 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C10orf55 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1	2	3
splice region						0
non coding			40	10	38	88
Total	0	0	40	11	40

Variants in C10orf55

This is a list of pathogenic ClinVar variants found in the C10orf55 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-73911209-G-A		Quebec platelet disorder	Uncertain significance (Jan 13, 2018)
10-73911218-G-A		Quebec platelet disorder	Uncertain significance (Jan 13, 2018)
10-73911227-C-G		Quebec platelet disorder	Uncertain significance (Jan 13, 2018)
10-73911404-G-T			Benign (Jun 19, 2021)
10-73911531-C-T		Quebec platelet disorder	Benign/Likely benign (Oct 01, 2023)
10-73911536-A-G		Quebec platelet disorder	Benign (Jan 12, 2018)
10-73911538-C-A		Quebec platelet disorder	Benign (Jan 12, 2018)
10-73911572-C-A		Quebec platelet disorder • not specified	Conflicting classifications of pathogenicity (Sep 29, 2022)
10-73911598-G-T		Quebec platelet disorder	Benign (Jan 12, 2018)
10-73911618-T-C		Quebec platelet disorder	Likely benign (Jan 12, 2018)
10-73912117-G-A			Benign (Jun 19, 2021)
10-73912216-G-T		C10orf55-related disorder	Likely benign (May 17, 2021)
10-73912227-G-C		PLAU-related disorder	Uncertain significance (Sep 16, 2024)
10-73912240-A-G		Quebec platelet disorder	Benign (May 22, 2017)
10-73912272-T-A		Quebec platelet disorder	Uncertain significance (Jan 12, 2018)
10-73912291-A-G		Quebec platelet disorder • PLAU-related disorder	Benign/Likely benign (Mar 01, 2023)
10-73912292-A-G		Quebec platelet disorder • PLAU-related disorder	Benign (Jan 13, 2018)
10-73912301-G-A		Hirschsprung disease, susceptibility to, 1 • Quebec platelet disorder	Benign/Likely benign (Jun 01, 2024)
10-73912319-A-T		not specified	Uncertain significance (Jan 06, 2023)
10-73912619-G-GT			Benign (Jun 19, 2021)
10-73912620-G-T			Benign (Jun 19, 2021)
10-73912717-A-G			Benign (Jun 19, 2021)
10-73912917-C-G		C10orf55-related disorder	Likely benign (May 31, 2023)
10-73912924-A-G		Quebec platelet disorder	Uncertain significance (Jan 12, 2018)
10-73912966-G-A		Quebec platelet disorder	Benign (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C10orf55	protein_coding	protein_coding	ENST00000409178	2	12809

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0144	0.461	125717	0	3	125720	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.423	74	85.0	0.871	0.00000411	966
Missense in Polyphen		7	12.58	0.55642		117
Synonymous	1.38	24	34.3	0.699	0.00000184	328
Loss of Function	-0.801	2	1.10	1.83	4.66e-8	12

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.584
• rvis_EVS: 0.68
• rvis_percentile_EVS: 84.81

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S

Gene Damage Prediction

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