C1orf216

chromosome 1 open reading frame 216

Basic information

Region (hg38): 1:35713877-35718894

Links

ENSG00000142686 ∙ NCBI:127703 ∙ ∙ HGNC:26800 ∙ Uniprot:Q8TAB5 ∙ 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 C1orf216 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1orf216 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in C1orf216

This is a list of pathogenic ClinVar variants found in the C1orf216 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-35715814-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-35716264-G-A		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1orf216	protein_coding	protein_coding	ENST00000270815	1	5598

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00134	0.672	125492	1	255	125748	0.00102

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.113	129	133	0.972	0.00000695	1497
Missense in Polyphen		50	44.27	1.1294		548
Synonymous	-0.0807	56	55.2	1.01	0.00000300	476
Loss of Function	0.694	5	6.98	0.716	3.90e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000607	0.000602
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00375	0.00370
European (Non-Finnish)	0.00139	0.00135
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000992	0.000978

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0933

Intolerance Scores

• loftool: 0.233
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.01

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.170
• ghis: 0.452

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: 5730409E04Rik

Gene ontology

• Molecular function: protein binding