C22orf42

chromosome 22 open reading frame 42

Basic information

Region (hg38): 22:32149006-32159322

Links

ENSG00000205856 ∙ NCBI:150297 ∙ ∙ HGNC:27160 ∙ Uniprot:Q6IC83 ∙ 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 C22orf42 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C22orf42 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 C22orf42

This is a list of pathogenic ClinVar variants found in the C22orf42 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-32149769-T-G		not specified	Uncertain significance (Oct 22, 2021)
22-32154268-C-T		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C22orf42	protein_coding	protein_coding	ENST00000382097	9	10317

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.12e-14	0.00508	125623	0	125	125748	0.000497

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0316	147	146	1.01	0.00000829	1637
Missense in Polyphen		21	16.147	1.3005		119
Synonymous	0.615	49	54.8	0.894	0.00000354	463
Loss of Function	-0.865	18	14.4	1.25	8.11e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00208	0.00207
Ashkenazi Jewish	0.000112	0.0000992
East Asian	0.000544	0.000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000321	0.000316
Middle Eastern	0.000544	0.000544
South Asian	0.000213	0.000196
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.902
• rvis_EVS: 1.04
• rvis_percentile_EVS: 91.26

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146

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