C4orf46

chromosome 4 open reading frame 46

Basic information

Region (hg38): 4:158666674-158672255

Links

ENSG00000205208 ∙ NCBI:201725 ∙ OMIM:616210 ∙ HGNC:27320 ∙ Uniprot:Q504U0 ∙ 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 C4orf46 gene.

• not provided (2 variants)
• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C4orf46 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					1	1
missense			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	2	1	1

Variants in C4orf46

This is a list of pathogenic ClinVar variants found in the C4orf46 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-158669744-G-T		not specified	Uncertain significance (Nov 09, 2021)
4-158671796-G-T			Benign (Jun 14, 2018)
4-158671797-G-C		not specified	Uncertain significance (Aug 12, 2021)
4-158671871-G-C			Likely benign (Sep 17, 2018)
4-158672031-A-G			Likely benign (Sep 17, 2018)
4-158672047-A-G			Likely benign (Sep 17, 2018)
4-158672142-G-A		Multiple acyl-CoA dehydrogenase deficiency	Uncertain significance (Jun 14, 2016)
4-158672218-G-A		Multiple acyl-CoA dehydrogenase deficiency	Likely benign (Sep 17, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C4orf46	protein_coding	protein_coding	ENST00000379205	2	5577

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0396	0.664	125426	6	295	125727	0.00120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.239	62	56.9	1.09	0.00000294	705
Missense in Polyphen		28	27.892	1.0039		357
Synonymous	-0.617	28	24.1	1.16	0.00000117	244
Loss of Function	0.458	2	2.83	0.706	1.19e-7	41

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0355	0.0180
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000979	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000653	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.407
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.144
• ghis: 0.605

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: 4930579G24Rik

Gene ontology

• Cellular component: cytoplasm
• Molecular function: protein binding