C1orf56

protein-coding

chromosome 1 open reading frame 56

Gene summary

This gene is a proto-oncogene whose promoter is methylated by DNA methyltransferase 3B (DNMT3B), which represses the proto-oncogene. However, a catalytically inactive isoform of DNMT3B is overexpressed in lymphomas, leading to hypomethylation of the proto-oncogene's promoter and derepression of the proto-oncogene. [provided by RefSeq, Sep 2016]

MANE transcript

NM_017860.5

Inheritance

—

ClinVar variants

U:6B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr1:151,047,751-151,051,986

External References & Databases

Ensembl (ENSG00000143443)

Transcript & Mutation Effects

hg38 • Region Span ~4.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to C1orf56 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017860.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			4 clinvar	1 clinvar		5
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	6	1	0	7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017860.5	RefSeq	NP_060330.2	2	MANE Select
ENST00000368926.6	Ensembl	ENSP00000357922.5	2	MANE Select
ENST00001120029.1	Ensembl	ENSP00000789834.1	2	Standard
ENST00001145011.1	Ensembl	ENSP00000809481.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in leukocytes - TarBase
miR-targeted genes in lymphocytes - TarBase

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368926
Coding exons: 2
Length: 4247
Individuals with no LoFs: 125151
Homozygous LoFs: 2
Heterozygous LoFs: 593
Defined: 125746
p: 0.00237

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.229	187	196	0.954	0.00000885	2170
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.00022	0.00022	rare
Finnish	0.012	0.012	notable
European (Non-Finnish)	0.0026	0.0026	notable
South Asian	0.00017	0.00016	rare
Other	0.0023	0.0023	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in control of cellular proliferation. Onconcogenic modifier contributing to the tumor suppressor function of DNMT3B. {ECO:0000269|PubMed:22133874}.;

Recessive Scores

pRec: 0.0719

Intolerance Scores

LoFtool: 0.307
RVIS EVS: 0.33
RVIS percentile EVS: 73.27

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N

Gene Damage Prediction

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