C2orf16

chromosome 2 open reading frame 16

Basic information

Region (hg38): 2:27537385-27582722

Links

ENSG00000221843 ∙ NCBI:84226 ∙ ∙ HGNC:25275 ∙ Uniprot:Q68DN1 ∙ 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 C2orf16 gene.

• Inborn genetic diseases (16 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C2orf16 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				4		4
missense			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	6	0

Variants in C2orf16

This is a list of pathogenic ClinVar variants found in the C2orf16 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-27576598-A-G		not specified	Uncertain significance (Sep 15, 2021)
2-27576768-A-G		not specified	Uncertain significance (Nov 16, 2021)
2-27577372-C-T		not specified	Uncertain significance (Oct 13, 2021)
2-27577792-G-C		not specified	Likely benign (Oct 06, 2021)
2-27577819-C-A		not specified	Uncertain significance (Oct 12, 2021)
2-27578308-C-G		not specified	Uncertain significance (Nov 08, 2021)
2-27578350-T-C		not specified	Uncertain significance (Jul 14, 2021)
2-27578414-T-C			Likely benign (Feb 01, 2023)
2-27579884-C-T			Likely benign (Jul 01, 2022)
2-27580140-C-T		not specified	Uncertain significance (Aug 12, 2021)
2-27580222-T-C			Likely benign (Mar 01, 2023)
2-27580535-T-C			Likely benign (May 01, 2022)
2-27581391-C-T		not specified	Uncertain significance (Sep 14, 2021)
2-27581943-C-T		not specified	Uncertain significance (Nov 05, 2021)
2-27582040-G-A		not specified	Uncertain significance (Aug 16, 2021)
2-27582145-A-G		not specified	Uncertain significance (Aug 12, 2021)
2-27582228-C-T		not specified	Uncertain significance (Sep 17, 2021)
2-27582279-A-G		not specified	Uncertain significance (Jul 20, 2021)
2-27582298-G-T		not specified	Uncertain significance (Jul 20, 2021)
2-27582347-T-C			Likely benign (Mar 01, 2023)
2-27582370-G-C		not specified	Uncertain significance (Jul 08, 2021)
2-27582409-C-G		not specified	Uncertain significance (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C2orf16	protein_coding	protein_coding	ENST00000408964	1	6200

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.34e-14	0.490	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.318	989	1.02e+3	0.972	0.0000552	12901
Missense in Polyphen		152	153.49	0.99031		2349
Synonymous	-1.24	395	365	1.08	0.0000187	3993
Loss of Function	1.54	27	37.1	0.728	0.00000197	485

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.866
• rvis_EVS: 1.31
• rvis_percentile_EVS: 94

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.403

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	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: 4932415D10Rik

Gene ontology

• Cellular component: nucleus;extracellular exosome