C12orf50

chromosome 12 open reading frame 50

Basic information

Region (hg38): 12:87980035-88034037

Links

ENSG00000165805 ∙ NCBI:160419 ∙ ∙ HGNC:26665 ∙ Uniprot:Q8NA57 ∙ 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 C12orf50 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C12orf50 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 C12orf50

This is a list of pathogenic ClinVar variants found in the C12orf50 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-87983180-G-A		not specified	Uncertain significance (May 01, 2024)
12-87986012-G-A		not specified	Uncertain significance (Sep 17, 2021)
12-87986336-A-G		not specified	Uncertain significance (Aug 23, 2021)
12-87994677-A-G		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C12orf50	protein_coding	protein_coding	ENST00000298699	12	53999

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.73e-7	0.991	125701	0	38	125739	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.158	220	214	1.03	0.0000106	2729
Missense in Polyphen		66	63.9	1.0329		914
Synonymous	-0.223	77	74.5	1.03	0.00000389	716
Loss of Function	2.38	15	28.8	0.521	0.00000171	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000398	0.000395
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000326	0.000323
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.000109	0.000109
South Asian	0.000133	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.790
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.49

Haploinsufficiency Scores

• pHI: 0.448
• hipred: N
• hipred_score: 0.421

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: 1700017N19Rik

Gene ontology

• Biological process: poly(A)+ mRNA export from nucleus
• Cellular component: transcription export complex
• Molecular function: mRNA binding;protein binding