C5orf46

chromosome 5 open reading frame 46

Basic information

Region (hg38): 5:147880725-147906538

Links

ENSG00000178776 ∙ NCBI:389336 ∙ ∙ HGNC:33768 ∙ Uniprot:Q6UWT4 ∙ 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 C5orf46 gene.

• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C5orf46 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						0
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	1	0	0

Variants in C5orf46

This is a list of pathogenic ClinVar variants found in the C5orf46 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-147881517-C-A		not specified	Uncertain significance (Apr 27, 2024)
5-147881541-C-G		not specified	Uncertain significance (Oct 05, 2022)
5-147881556-C-A		not specified	Uncertain significance (Apr 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C5orf46	protein_coding	protein_coding	ENST00000318315	3	25813

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0720	0.755	125590	0	16	125606	0.0000637

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.328	42	48.4	0.867	0.00000278	557
Missense in Polyphen		1	3.4942	0.28619		38
Synonymous	-1.13	26	19.6	1.32	0.00000119	167
Loss of Function	0.956	2	4.09	0.490	2.69e-7	52

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000242	0.000241
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000618	0.0000616
Middle Eastern	0.00	0.00
South Asian	0.0000992	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.394
• rvis_EVS: 0.3
• rvis_percentile_EVS: 72.01

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.405

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gm94

Gene ontology

• Biological process: biological_process
• Cellular component: extracellular exosome
• Molecular function: molecular_function