C22orf15

chromosome 22 open reading frame 15

Basic information

Region (hg38): 22:23762990-23765863

Links

ENSG00000169314 ∙ NCBI:150248 ∙ ∙ HGNC:15558 ∙ Uniprot:Q8WYQ4 ∙ 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 C22orf15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C22orf15 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					2	2
Total	0	0	4	0	2

Variants in C22orf15

This is a list of pathogenic ClinVar variants found in the C22orf15 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-23763324-G-A		not specified	Uncertain significance (Oct 18, 2021)
22-23764306-G-C		not specified	Uncertain significance (Oct 27, 2021)
22-23764377-A-G		not specified	Uncertain significance (Oct 27, 2021)
22-23764802-G-T		not specified	Uncertain significance (Sep 27, 2021)
22-23765747-C-T			Benign (Sep 29, 2018)
22-23765813-C-G			Benign (Oct 17, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C22orf15	protein_coding	protein_coding	ENST00000402217	6	2841

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00279	0.815	125704	0	34	125738	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.648	73	90.3	0.808	0.00000539	938
Missense in Polyphen		12	20.589	0.58284		269
Synonymous	0.426	32	35.2	0.909	0.00000176	312
Loss of Function	1.09	5	8.42	0.594	4.40e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000423	0.000423
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000326	0.000326
South Asian	0.00	0.00
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.638
• rvis_EVS: 0.59
• rvis_percentile_EVS: 82.45

Haploinsufficiency Scores

• pHI: 0.166
• 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: Gm867