C16orf89

protein-coding

chromosome 16 open reading frame 89

Gene summary

This gene is expressed predominantly in the thyroid. Based on expression patterns similar to thyroid transcription factors and proteins, this gene may function in the development and function of the thyroid. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

MANE transcript

NM_001098514.3

Inheritance

—

ClinVar variants

U:8B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.21

Max pathogenic AF

—

Genomic locus

chr16:5,044,122-5,066,110

External References & Databases

Ensembl (ENSG00000153446)

Transcript & Mutation Effects

hg38 • Region Span ~22.0 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 C16orf89 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 6

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001098514.3. 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			1 clinvar	1 clinvar		2
missense			3 clinvar	1 clinvar		4
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	8	2	0	10

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001098514.3	RefSeq	NP_001091984.2	8	MANE Select
ENST00000472572.8	Ensembl	ENSP00000420566.2	8	MANE Select
NM_152459.5	RefSeq	NP_689672.4	8	Standard
ENST00000315997.5	Ensembl	ENSP00000324672.5	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein homodimerization activity

Cellular Component

cytosol
membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000315997
Coding exons: 8
Length: 21989
Individuals with no LoFs: 124677
Homozygous LoFs: 0
Heterozygous LoFs: 126
Defined: 124803
p: 0.000505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.51	273	211	1.29	0.0000120	2565
Missense (PolyPhen)		62	48.762	1.2715		639
Synonymous	-1.49	112	93.7	1.20	0.00000566	802
Loss of Function	-0.814	22	18.3	1.21	8.68e-7	199

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00020	0.00019	rare
Latino/Admixed American	0.0013	0.0013	notable
Ashkenazi Jewish	0.0029	0.0029	notable
East Asian	0.00034	0.00033	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00021	0.00021	rare
South Asian	0.00049	0.00049	rare
Other	0.00066	0.00066	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.880
RVIS EVS: 0.8
RVIS percentile EVS: 87.66

Essentials

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

Gene Damage Prediction

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