C2orf50

chromosome 2 open reading frame 50

Basic information

Region (hg38): 2:11133128-11151317

Links

ENSG00000150873 ∙ NCBI:130813 ∙ ∙ HGNC:26324 ∙ Uniprot:Q96LR7 ∙ 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 C2orf50 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C2orf50 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C2orf50	protein_coding	protein_coding	ENST00000381585	3	13738

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000117	0.396	125634	0	110	125744	0.000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.177	95	90.3	1.05	0.00000493	1029
Missense in Polyphen		20	23.425	0.8538		258
Synonymous	-0.293	39	36.7	1.06	0.00000192	338
Loss of Function	0.106	6	6.29	0.954	3.20e-7	62

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000283	0.000273
Ashkenazi Jewish	0.000508	0.000496
East Asian	0.000447	0.000435
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.000331	0.000316
Middle Eastern	0.000447	0.000435
South Asian	0.00179	0.00177
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.447
• rvis_EVS: 0.9
• rvis_percentile_EVS: 89.39

Haploinsufficiency Scores

• pHI: 0.201
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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: 2410004P03Rik

Gene ontology

• Molecular function: protein binding