C16orf89

chromosome 16 open reading frame 89

Basic information

Region (hg38): 16:5044122-5066110

Links

ENSG00000153446 ∙ NCBI:146556 ∙ ∙ HGNC:28687 ∙ Uniprot:Q6UX73 ∙ 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 C16orf89 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C16orf89 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			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in C16orf89

This is a list of pathogenic ClinVar variants found in the C16orf89 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-5058503-C-T		not specified	Uncertain significance (Jul 12, 2024)
16-5060315-GT-G		not specified	Uncertain significance (Jan 23, 2024)
16-5062443-C-T		not specified	Uncertain significance (Aug 13, 2021)
16-5065720-C-T		not specified	Likely benign (Jul 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C16orf89	protein_coding	protein_coding	ENST00000315997	8	21989

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.63e-16	0.00180	124677	0	126	124803	0.000505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.51	273	211	1.29	0.0000120	2565
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00148	0.00147
Ashkenazi Jewish	0.00290	0.00288
East Asian	0.000337	0.000334
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000213	0.000212
Middle Eastern	0.000337	0.000334
South Asian	0.000491	0.000490
Other	0.000663	0.000660

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.880
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.66

Haploinsufficiency Scores

• 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: AU021092
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); renal/urinary system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Cellular component: cytosol;membrane;extracellular exosome
• Molecular function: protein homodimerization activity