C6orf89

protein-coding

chromosome 6 open reading frame 89

Gene summary

Involved in several processes, including epithelial cell proliferation; positive regulation of cell cycle; and wound healing. Located in several cellular components, including Golgi membrane; midbody; and nucleolus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001286635.2

Inheritance

—

ClinVar variants

U:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr6:36,871,870-36,928,964

External References & Databases

Ensembl (ENSG00000198663)

Transcript & Mutation Effects

hg38 • Region Span ~57.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to C6orf89 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001286635.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			3 clinvar			3
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	8	0	0	8

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 72 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001286635.2	RefSeq	NP_001273564.1	7	MANE Select
ENST00000480824.7	Ensembl	ENSP00000475947.1	7	MANE Select
NM_001286636.2	RefSeq	NP_001273565.1	6	Standard
NM_001286637.2	RefSeq	NP_001273566.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

wound healing
positive regulation of cell cycle
epithelial cell proliferation
positive regulation of histone deacetylase activity

Molecular Function

protein binding

Cellular Component

Golgi membrane
nucleolus
cytoplasm
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000355190
Coding exons: 8
Length: 57095
Individuals with no LoFs: 125719
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125748
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.501	178	198	0.900	0.0000103	2330
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0.00033	0.00033	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N

Gene Damage Prediction

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