C22orf23

chromosome 22 open reading frame 23

Basic information

Region (hg38): 22:37943050-37953669

Links

ENSG00000128346 ∙ NCBI:84645 ∙ OMIM:619678 ∙ HGNC:18589 ∙ Uniprot:Q9BZE7 ∙ 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 C22orf23 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C22orf23 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						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in C22orf23

This is a list of pathogenic ClinVar variants found in the C22orf23 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-37947314-A-T		not specified	Uncertain significance (Nov 05, 2021)
22-37951497-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C22orf23	protein_coding	protein_coding	ENST00000249079	6	10149

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.68e-14	0.00367	125382	2	363	125747	0.00145

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.306	117	127	0.923	0.00000685	1416
Missense in Polyphen		33	37.343	0.88369		435
Synonymous	-0.00644	44	43.9	1.00	0.00000212	413
Loss of Function	-1.03	18	13.8	1.30	9.41e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00217	0.00210
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.000647	0.000647
European (Non-Finnish)	0.00228	0.00228
Middle Eastern	0.000272	0.000272
South Asian	0.000730	0.000719
Other	0.00183	0.00179

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.857
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.0419
• hipred: N
• hipred_score: 0.144
• ghis: 0.454

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: 1700088E04Rik

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function;protein binding