C5orf58

chromosome 5 open reading frame 58

Basic information

Region (hg38): 5:170229104-170252575

Links

ENSG00000234511 ∙ NCBI:133874 ∙ ∙ HGNC:37272 ∙ Uniprot:C9J3I9 ∙ 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 C5orf58 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C5orf58 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3	1	1	5
Total	0	0	4	1	1

Variants in C5orf58

This is a list of pathogenic ClinVar variants found in the C5orf58 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-170246034-A-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
5-170246108-A-C		not specified	Uncertain significance (Oct 06, 2021)
5-170248719-G-A		not specified	Uncertain significance (Jan 04, 2024)
5-170248735-A-G			Likely benign (Jun 01, 2022)
5-170252350-C-T		not specified	Benign (Jan 24, 2024)
5-170252456-G-A			Uncertain significance (Jul 01, 2022)
5-170252478-T-C		Immunodeficiency 81	Uncertain significance (Nov 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C5orf58	protein_coding	protein_coding	ENST00000521850	3	20129

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0464	0.692	124574	0	9	124583	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.395	39	46.6	0.837	0.00000205	670
Missense in Polyphen		6	7.6564	0.78366		112
Synonymous	-0.380	19	17.0	1.12	7.98e-7	185
Loss of Function	0.599	2	3.15	0.636	1.32e-7	50

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000936	0.0000936
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000625	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.00000885	0.00000885
Middle Eastern	0.0000625	0.0000556
South Asian	0.000131	0.000131
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.677
• rvis_EVS: 0.26
• rvis_percentile_EVS: 69.83

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.153
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N

Gene Damage Prediction

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