C6orf89

chromosome 6 open reading frame 89

Basic information

Region (hg38): 6:36871870-36928964

Links

ENSG00000198663 ∙ NCBI:221477 ∙ OMIM:616642 ∙ HGNC:21114 ∙ Uniprot:Q6UWU4 ∙ 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 C6orf89 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C6orf89 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						0
Total	0	0	1	0	0

Variants in C6orf89

This is a list of pathogenic ClinVar variants found in the C6orf89 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-36874758-G-T			Likely benign (Jan 01, 2024)
6-36874763-T-C		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
6-36902362-A-T		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C6orf89	protein_coding	protein_coding	ENST00000355190	8	57095

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.78e-7	0.766	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.501	178	198	0.900	0.0000103	2330
Missense in Polyphen		55	61.909	0.8884		797
Synonymous	-0.301	77	73.7	1.04	0.00000423	664
Loss of Function	1.29	12	17.9	0.671	8.47e-7	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000326	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000326	0.000326
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits histone deacetylase (HDAC) enhancer properties (PubMed:23460338). May play a role in cell cycle progression and wound repair of bronchial epithelial cells (PubMed:21857995). {ECO:0000269|PubMed:21857995, ECO:0000269|PubMed:23460338}.

Recessive Scores

• pRec: 0.339

Intolerance Scores

• loftool: 0.376
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.36

Haploinsufficiency Scores

• pHI: 0.322
• hipred: N
• hipred_score: 0.169
• ghis: 0.466

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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: BC004004
• Phenotype: normal phenotype

Gene ontology

• Biological process: wound healing;positive regulation of cell cycle;epithelial cell proliferation;positive regulation of histone deacetylase activity
• Cellular component: Golgi membrane;nucleolus;cytoplasm;plasma membrane;integral component of membrane;midbody
• Molecular function: protein binding