C6orf58

chromosome 6 open reading frame 58

Basic information

Region (hg38): 6:127519455-127591820

Links

ENSG00000184530 ∙ NCBI:352999 ∙ ∙ HGNC:20960 ∙ Uniprot:Q6P5S2 ∙ 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 C6orf58 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C6orf58 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in C6orf58

This is a list of pathogenic ClinVar variants found in the C6orf58 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-127577406-A-G		not specified	Uncertain significance (Nov 16, 2021)
6-127578709-A-G		not specified	Uncertain significance (Aug 16, 2021)
6-127590307-A-G		not specified	Uncertain significance (Oct 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C6orf58	protein_coding	protein_coding	ENST00000329722	6	72363

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.10e-9	0.266	125638	0	10	125648	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.187	161	168	0.959	0.00000761	2165
Missense in Polyphen		55	56.843	0.96757		783
Synonymous	-0.621	66	59.9	1.10	0.00000282	604
Loss of Function	0.602	14	16.7	0.841	8.60e-7	195

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000186	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000203	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.00000891	0.00000880
Middle Eastern	0.000203	0.000163
South Asian	0.0000985	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in early liver development. {ECO:0000250|UniProtKB:A5PF61, ECO:0000250|UniProtKB:Q4QRF7}.

Intolerance Scores

• loftool: 0.847
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.0600
• hipred: N
• hipred_score: 0.123

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: 2310057J18Rik

Zebrafish Information Network

• Gene name: leg1.2
• Affected structure: liver
• Phenotype tag: abnormal
• Phenotype quality: decreased size