C10orf105

chromosome 10 open reading frame 105

Basic information

Region (hg38): 10:71711700-71737824

Links

ENSG00000214688 ∙ NCBI:414152 ∙ ∙ HGNC:20304 ∙ Uniprot:Q8TEF2 ∙ 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 C10orf105 gene.

• not provided (62 variants)
• Usher syndrome type 1 (16 variants)
• not specified (13 variants)
• Usher syndrome type 1D (9 variants)
• Autosomal recessive nonsyndromic hearing loss 12 (7 variants)
• Inborn genetic diseases (4 variants)
• Retinal dystrophy (3 variants)
• Usher syndrome type 1D;Autosomal recessive nonsyndromic hearing loss 12;Pituitary adenoma 5, multiple types (2 variants)
• CDH23-Related Disorders (2 variants)
• Retinitis pigmentosa-deafness syndrome (1 variants)
• Pituitary adenoma 5, multiple types (1 variants)
• Pituitary adenoma 5, multiple types;Usher syndrome type 1D;Autosomal recessive nonsyndromic hearing loss 12 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C10orf105 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				1		1
missense				1		1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	3	2	23	27	4	59
Total	3	2	23	29	4

Highest pathogenic variant AF is 0.00000657

Variants in C10orf105

This is a list of pathogenic ClinVar variants found in the C10orf105 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-71712645-T-A			Likely benign (Dec 12, 2022)
10-71712656-C-T			Likely benign (Jan 25, 2024)
10-71712658-C-G			Likely benign (Sep 19, 2022)
10-71712658-C-T		Usher syndrome type 1	Likely benign (Jan 17, 2024)
10-71712661-A-T			Likely benign (Nov 19, 2023)
10-71712663-A-G			Pathogenic (Feb 01, 2018)
10-71712666-C-T			Likely benign (Aug 07, 2023)
10-71712669-C-T			Likely benign (Dec 13, 2023)
10-71712670-G-A			Uncertain significance (Jul 30, 2022)
10-71712670-G-C			Uncertain significance (Mar 24, 2022)
10-71712672-C-A			Likely benign (Oct 13, 2023)
10-71712672-C-G			Likely benign (Nov 01, 2023)
10-71712674-C-G			Uncertain significance (Feb 28, 2022)
10-71712674-C-T		not specified • Retinal dystrophy • Usher syndrome type 1	Conflicting classifications of pathogenicity (Jan 16, 2024)
10-71712675-T-G			Likely benign (Jan 04, 2024)
10-71712676-G-C		Inborn genetic diseases	Uncertain significance (Feb 21, 2024)
10-71712684-G-A			Likely benign (May 11, 2020)
10-71712685-C-T		Inborn genetic diseases • Usher syndrome type 1D • Usher syndrome type 1	Pathogenic (Nov 03, 2023)
10-71712686-G-A			Uncertain significance (Aug 28, 2021)
10-71712687-A-C			Likely benign (Feb 13, 2023)
10-71712692-C-G			Uncertain significance (Oct 16, 2023)
10-71712692-C-T		Usher syndrome type 1	Uncertain significance (Jul 26, 2022)
10-71712693-G-A		not specified • Usher syndrome type 1D • Autosomal recessive nonsyndromic hearing loss 12 • Usher syndrome type 1	Conflicting classifications of pathogenicity (Jan 31, 2024)
10-71712694-G-T		Usher syndrome type 1	Uncertain significance (Mar 01, 2016)
10-71712695-G-A			Uncertain significance (Jul 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C10orf105	protein_coding	protein_coding	ENST00000441508	1	26124

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0842	0.571	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.202	71	66.4	1.07	0.00000452	845
Missense in Polyphen		15	18.275	0.82079		285
Synonymous	-1.69	40	28.5	1.40	0.00000196	292
Loss of Function	-0.159	1	0.842	1.19	3.56e-8	13

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	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.21
• rvis_percentile_EVS: 93.07

Haploinsufficiency Scores

• pHI: 0.140

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: 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: Gm17455

Gene ontology

• Cellular component: integral component of membrane