C4orf47

chromosome 4 open reading frame 47

Basic information

Region (hg38): 4:185426248-185449826

Links

ENSG00000205129 ∙ NCBI:441054 ∙ ∙ HGNC:34346 ∙ Uniprot:A7E2U8 ∙ 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 C4orf47 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C4orf47 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			5			5
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	7	1	0

Variants in C4orf47

This is a list of pathogenic ClinVar variants found in the C4orf47 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-185432048-A-T		not specified	Uncertain significance (Oct 06, 2021)
4-185436338-T-G		not specified	Uncertain significance (Jun 23, 2021)
4-185445010-C-G		not specified	Uncertain significance (Dec 14, 2023)
4-185445023-TG-T			Likely benign (Jan 01, 2018)
4-185445102-G-A		not specified	Uncertain significance (Aug 13, 2021)
4-185445507-G-A		not specified	Uncertain significance (Jan 10, 2023)
4-185445524-T-C		not specified	Uncertain significance (Jan 16, 2024)
4-185449630-G-C		not specified	Uncertain significance (Aug 04, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C4orf47	protein_coding	protein_coding	ENST00000378850	7	23587

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000621	0.914	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	101	142	0.709	0.00000683	2010
Missense in Polyphen		29	46.154	0.62834		683
Synonymous	0.0165	50	50.1	0.997	0.00000264	571
Loss of Function	1.53	7	12.9	0.542	7.33e-7	203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.79
• rvis_percentile_EVS: 87.34

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: 1700029J07Rik

Gene ontology

• Cellular component: cytoplasm;centrosome