C10orf67

chromosome 10 open reading frame 67

Basic information

Region (hg38): 10:23202696-23344845

Previous symbols: [ "LINC01552", "C10orf115" ]

Links

ENSG00000179133 ∙ NCBI:256815 ∙ ∙ HGNC:28716 ∙ Uniprot:Q8IYJ2 ∙ 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 C10orf67 gene.

• Pancreatic agenesis 2 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C10orf67 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1				2	3
Total	1	0	1	0	2

Variants in C10orf67

This is a list of pathogenic ClinVar variants found in the C10orf67 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-23219094-G-A			Benign (Nov 12, 2018)
10-23219508-A-G		Pancreatic agenesis 2	Pathogenic (Feb 12, 2023)
10-23219800-C-T			Benign (Nov 12, 2018)
10-23233560-C-T		Type 2 diabetes mellitus	Benign (-)
10-23255343-T-C		Type 2 diabetes mellitus	Benign (-)
10-23259604-C-A		Type 2 diabetes mellitus	Benign (-)
10-23283453-A-C		Type 2 diabetes mellitus	Benign (-)
10-23290495-G-A		Type 2 diabetes mellitus	Benign (-)
10-23344755-C-T		not specified	Uncertain significance (Aug 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C10orf67	protein_coding	protein_coding	ENST00000323327	5	77651

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.80e-8	0.0708	124567	0	39	124606	0.000157

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.266	86	93.2	0.922	0.00000422	1206
Missense in Polyphen		23	26.784	0.85873		398
Synonymous	0.900	28	34.7	0.806	0.00000159	332
Loss of Function	-0.468	11	9.45	1.16	4.84e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000232	0.000232
Ashkenazi Jewish	0.00	0.00
East Asian	0.00123	0.00122
Finnish	0.00	0.00
European (Non-Finnish)	0.0000535	0.0000531
Middle Eastern	0.00123	0.00122
South Asian	0.0000654	0.0000654
Other	0.000170	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.501
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.123
• ghis: 0.465

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: 4921504E06Rik

Gene ontology

• Cellular component: mitochondrion
• Molecular function: protein binding