C2orf80

chromosome 2 open reading frame 80

Basic information

Region (hg38): 2:208165343-208190030

Links

ENSG00000188674 ∙ NCBI:389073 ∙ OMIM:615536 ∙ HGNC:34352 ∙ Uniprot:Q0P641 ∙ 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 C2orf80 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C2orf80 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in C2orf80

This is a list of pathogenic ClinVar variants found in the C2orf80 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-208171034-T-C		not specified	Uncertain significance (Aug 13, 2021)
2-208180784-A-C		not specified	Uncertain significance (Sep 17, 2021)
2-208181258-C-T		not specified	Uncertain significance (Oct 12, 2021)
2-208183013-T-C		not specified	Uncertain significance (Oct 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C2orf80	protein_coding	protein_coding	ENST00000341287	8	24731

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.50e-11	0.0392	124570	0	224	124794	0.000898

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.101	109	106	1.03	0.00000546	1245
Missense in Polyphen		36	34.551	1.0419		434
Synonymous	-1.31	45	35.1	1.28	0.00000176	356
Loss of Function	-0.243	15	14.0	1.07	7.76e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000607	0.000607
Ashkenazi Jewish	0.00	0.00
East Asian	0.00784	0.00787
Finnish	0.00121	0.00121
European (Non-Finnish)	0.000256	0.000256
Middle Eastern	0.00784	0.00787
South Asian	0.000327	0.000327
Other	0.000331	0.000330

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.733
• rvis_EVS: 0.77
• rvis_percentile_EVS: 87.01

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.420

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: D630023F18Rik
• Phenotype: skeleton phenotype; immune system phenotype; vision/eye phenotype; pigmentation phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)