C12orf56

chromosome 12 open reading frame 56

Basic information

Region (hg38): 12:64264762-64390758

Links

ENSG00000185306 ∙ NCBI:115749 ∙ ∙ HGNC:26967 ∙ Uniprot:Q8IXR9 ∙ 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 C12orf56 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C12orf56 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in C12orf56

This is a list of pathogenic ClinVar variants found in the C12orf56 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-64267227-G-A		not specified	Uncertain significance (Aug 10, 2021)
12-64270603-T-C		not specified	Uncertain significance (Oct 26, 2021)
12-64286039-T-A		not specified	Likely benign (Jun 18, 2021)
12-64318729-C-T		not specified	Uncertain significance (Jul 06, 2021)
12-64352999-G-A		not specified	Uncertain significance (Jul 06, 2021)
12-64390397-C-A		not specified	Uncertain significance (Aug 12, 2021)
12-64390457-C-T		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C12orf56	protein_coding	protein_coding	ENST00000333722	11	124756

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.89e-16	0.00421	124336	0	357	124693	0.00143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.125	227	232	0.977	0.0000125	3010
Missense in Polyphen		72	83.343	0.8639		1049
Synonymous	0.510	84	90.2	0.932	0.00000500	865
Loss of Function	-0.450	22	19.8	1.11	9.35e-7	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00162	0.00152
Ashkenazi Jewish	0.0000996	0.0000994
East Asian	0.00755	0.00753
Finnish	0.000144	0.000139
European (Non-Finnish)	0.00131	0.00130
Middle Eastern	0.00755	0.00753
South Asian	0.00120	0.00118
Other	0.000840	0.000825

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.237
• rvis_EVS: -0.25
• rvis_percentile_EVS: 36.07

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.208
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	Medium	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: D930020B18Rik