C16orf46

chromosome 16 open reading frame 46

Basic information

Region (hg38): 16:81053497-81077267

Links

ENSG00000166455 ∙ NCBI:123775 ∙ ∙ HGNC:26525 ∙ Uniprot:Q6P387 ∙ 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 C16orf46 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C16orf46 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in C16orf46

This is a list of pathogenic ClinVar variants found in the C16orf46 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-81061711-G-A		not specified	Uncertain significance (Aug 30, 2021)
16-81061822-G-A		not specified	Uncertain significance (Jul 15, 2021)
16-81063768-A-G		not specified	Uncertain significance (Sep 15, 2021)
16-81063950-A-T		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C16orf46	protein_coding	protein_coding	ENST00000299578	2	23771

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.81e-8	0.150	125660	0	87	125747	0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.42	268	210	1.28	0.0000110	2578
Missense in Polyphen		64	44.662	1.433		593
Synonymous	-0.169	88	86.0	1.02	0.00000502	801
Loss of Function	0.00163	11	11.0	0.999	5.38e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00102	0.00102
Ashkenazi Jewish	0.00179	0.00179
East Asian	0.000109	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000109	0.000109
South Asian	0.000555	0.000555
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.929
• rvis_EVS: 1.02
• rvis_percentile_EVS: 91.02

Haploinsufficiency Scores

• pHI: 0.0504
• hipred: N
• hipred_score: 0.123
• ghis: 0.428

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: 1700030J22Rik

Gene ontology

• Cellular component: nucleus;nucleoplasm;cytosol