C2orf73

chromosome 2 open reading frame 73

Basic information

Region (hg38): 2:54330034-54383742

Links

ENSG00000177994 ∙ NCBI:129852 ∙ ∙ HGNC:26861 ∙ Uniprot:Q8N5S3 ∙ 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 C2orf73 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C2orf73 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in C2orf73

This is a list of pathogenic ClinVar variants found in the C2orf73 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-54343763-T-C		not specified	Uncertain significance (Jul 26, 2021)
2-54358976-G-C		not specified	Uncertain significance (Aug 12, 2021)
2-54360231-T-G		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C2orf73	protein_coding	protein_coding	ENST00000398634	5	53709

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.67e-7	0.204	124622	0	15	124637	0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.574	150	131	1.14	0.00000617	1822
Missense in Polyphen		41	33.498	1.224		499
Synonymous	-1.50	60	46.9	1.28	0.00000249	527
Loss of Function	0.0785	10	10.3	0.974	4.31e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000116	0.0000994
East Asian	0.000228	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.0000361	0.0000354
Middle Eastern	0.000228	0.000223
South Asian	0.000164	0.000163
Other	0.000182	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.838
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.25

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

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: 4930505A04Rik