C1orf56

chromosome 1 open reading frame 56

Basic information

Region (hg38): 1:151047751-151051986

Links

ENSG00000143443 ∙ NCBI:54964 ∙ ∙ HGNC:26045 ∙ Uniprot:Q9BUN1 ∙ 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 C1orf56 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1orf56 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			2	1		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	2	1	0

Variants in C1orf56

This is a list of pathogenic ClinVar variants found in the C1orf56 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-151048058-A-G		not specified	Likely benign (Jul 14, 2021)
1-151048302-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-151048322-G-A		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1orf56	protein_coding	protein_coding	ENST00000368926	2	4247

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000969	0.349	125151	2	593	125746	0.00237

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.229	187	196	0.954	0.00000885	2170
Missense in Polyphen		38	53.03	0.71657		546
Synonymous	0.134	85	86.6	0.982	0.00000405	766
Loss of Function	0.242	8	8.78	0.912	3.83e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000536	0.000536
Ashkenazi Jewish	0.000497	0.000496
East Asian	0.000224	0.000217
Finnish	0.0120	0.0120
European (Non-Finnish)	0.00260	0.00259
Middle Eastern	0.000224	0.000217
South Asian	0.000165	0.000163
Other	0.00229	0.00228

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in control of cellular proliferation. Onconcogenic modifier contributing to the tumor suppressor function of DNMT3B. {ECO:0000269|PubMed:22133874}.
• Pathway: miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase (Consensus)

Recessive Scores

• pRec: 0.0719

Intolerance Scores

• loftool: 0.307
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.27

Haploinsufficiency Scores

• pHI: 0.0727
• hipred: N
• hipred_score: 0.204
• ghis: 0.416

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: Gm128
• Phenotype: reproductive system phenotype; normal phenotype