C22orf31

chromosome 22 open reading frame 31

Basic information

Region (hg38): 22:29058672-29061831

Links

ENSG00000100249 ∙ NCBI:25770 ∙ ∙ HGNC:26931 ∙ Uniprot:O95567 ∙ 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 C22orf31 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C22orf31 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						0
Total	0	0	4	0	0

Variants in C22orf31

This is a list of pathogenic ClinVar variants found in the C22orf31 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-29060434-G-C		not specified	Uncertain significance (Oct 22, 2021)
22-29060486-T-C		not specified	Uncertain significance (Oct 12, 2021)
22-29060720-C-A		Intellectual disability	Uncertain significance (Jan 28, 2020)
22-29060794-C-T		Intellectual disability	Uncertain significance (Jan 28, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C22orf31	protein_coding	protein_coding	ENST00000216071	3	3173

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.71e-7	0.245	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.186	163	156	1.04	0.00000809	1878
Missense in Polyphen		28	31.836	0.87949		445
Synonymous	-0.383	66	62.2	1.06	0.00000332	579
Loss of Function	0.305	11	12.1	0.906	7.88e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000822	0.000821
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000185	0.000176
Middle Eastern	0.000164	0.000163
South Asian	0.000294	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.844
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.37

Haploinsufficiency Scores

• pHI: 0.395
• hipred: N
• hipred_score: 0.123
• ghis: 0.438

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