C2orf69

chromosome 2 open reading frame 69

Basic information

Region (hg38): 2:199911292-199955935

Links

ENSG00000178074 ∙ NCBI:205327 ∙ OMIM:619219 ∙ HGNC:26799 ∙ Uniprot:Q8N8R5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• combined oxidative phosphorylation deficiency 53 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 53	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Allergy/Immunology/Infectious; Biochemical; Cardiovascular; Gastrointestinal; Neurologic	33945503; 34038740

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C2orf69 gene.

• Combined oxidative phosphorylation deficiency 53 (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C2orf69 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				4		4
missense			4	4		8
nonsense						0
start loss						0
frameshift	1	1				2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	1	4	8	0

Variants in C2orf69

This is a list of pathogenic ClinVar variants found in the C2orf69 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-199911443-G-T		Inborn genetic diseases	Uncertain significance (Jul 28, 2021)
2-199911455-T-C			Likely benign (Mar 01, 2022)
2-199911521-C-G		Inborn genetic diseases	Uncertain significance (Oct 19, 2022)
2-199911561-G-A			Likely benign (Oct 01, 2023)
2-199911622-G-GGAGCC		Combined oxidative phosphorylation deficiency 53	Likely pathogenic (Apr 07, 2023)
2-199911642-C-T			Likely benign (Apr 01, 2022)
2-199911684-G-A			Likely benign (Nov 01, 2022)
2-199911716-AG-A		Combined oxidative phosphorylation deficiency 53	Pathogenic (Jul 09, 2021)
2-199911732-GC-G		Combined oxidative phosphorylation deficiency 53	Pathogenic (Aug 01, 2021)
2-199911739-C-G			Uncertain significance (Jun 01, 2019)
2-199911748-CTCT-C		Combined oxidative phosphorylation deficiency 53	Pathogenic (Jul 09, 2021)
2-199911758-C-G			Uncertain significance (Jul 05, 2022)
2-199925103-A-G			Likely benign (Nov 01, 2022)
2-199925158-A-T		C2orf69-related disorder	Likely benign (Apr 01, 2022)
2-199925310-TTTTAA-T		Combined oxidative phosphorylation deficiency 53	Pathogenic (Jul 12, 2021)
2-199925570-AGAAAG-A		Combined oxidative phosphorylation deficiency 53	Pathogenic (Jul 09, 2021)
2-199925635-CATTCTGGAGGAAGCAAT-C		Combined oxidative phosphorylation deficiency 53	Pathogenic (Jul 09, 2021)
2-199925657-G-A		Combined oxidative phosphorylation deficiency 53	Pathogenic (Jul 09, 2021)
2-199925659-G-A		Inborn genetic diseases	Likely benign (Sep 05, 2022)
2-199925738-G-A			Likely benign (Nov 01, 2022)
2-199933071-T-A		not specified	Uncertain significance (Mar 18, 2024)
2-199933094-G-C		not specified	Uncertain significance (Mar 18, 2024)
2-199933116-C-T		not specified	Uncertain significance (Jun 01, 2023)
2-199933119-C-T		not specified	Uncertain significance (Feb 22, 2023)
2-199933165-T-G		not specified	Uncertain significance (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C2orf69	protein_coding	protein_coding	ENST00000319974	2	44680

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0187	0.963	124595	0	6	124601	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	164	211	0.778	0.0000101	2544
Missense in Polyphen		30	59.781	0.50183		792
Synonymous	0.217	76	78.4	0.969	0.00000368	729
Loss of Function	2.07	5	13.1	0.383	6.36e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000996	0.0000994
East Asian	0.0000556	0.0000556
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000266	0.0000266
Middle Eastern	0.0000556	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.144
• rvis_EVS: 0.39
• rvis_percentile_EVS: 75.87

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.199
• ghis: 0.437

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: 1700066M21Rik

Gene ontology

• Cellular component: extracellular region