C22orf39

chromosome 22 open reading frame 39

Basic information

Region (hg38): 22:19351368-19447711

Links

ENSG00000242259 ∙ NCBI:128977 ∙ ∙ HGNC:27012 ∙ Uniprot:Q6P5X5 ∙ 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 C22orf39 gene.

• not provided (67 variants)
• Inborn genetic diseases (32 variants)
• Malignant tumor of prostate (1 variants)
• HIRA-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C22orf39 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			2	4	1	7
splice region						0
non coding			38	23	32	93
Total	0	0	40	27	33

Variants in C22orf39

This is a list of pathogenic ClinVar variants found in the C22orf39 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-19351400-C-T			Likely benign (Jun 06, 2018)
22-19353365-C-A		not specified	Uncertain significance (Feb 12, 2024)
22-19353365-C-T			Likely benign (Aug 14, 2018)
22-19353375-T-C			Likely benign (Dec 31, 2019)
22-19353376-G-A		not specified	Uncertain significance (Sep 13, 2023)
22-19353386-G-A		not specified	Uncertain significance (Nov 14, 2023)
22-19353405-G-A		HIRA-related disorder	Benign (Dec 31, 2019)
22-19353483-A-G			Benign (Dec 31, 2019)
22-19353492-G-C		not specified	Uncertain significance (Feb 13, 2024)
22-19353500-G-A		not specified	Uncertain significance (Nov 09, 2023)
22-19353502-G-A		not specified	Uncertain significance (Jul 20, 2022)
22-19353518-A-G		not specified	Uncertain significance (Aug 17, 2021)
22-19354025-C-T			Benign (Dec 31, 2019)
22-19354026-G-A		not specified	Uncertain significance (Feb 23, 2023)
22-19354106-A-C			Benign (Dec 31, 2019)
22-19355751-C-T		HIRA-related disorder	Benign (Dec 31, 2019)
22-19355775-G-A		not specified	Uncertain significance (Feb 23, 2023)
22-19355789-C-T		HIRA-related disorder	Likely benign (Sep 17, 2019)
22-19355800-C-T		not specified	Uncertain significance (Jan 30, 2024)
22-19355801-G-A			Likely benign (Jul 16, 2018)
22-19355831-C-T			Likely benign (Aug 16, 2018)
22-19355853-G-A		not specified	Uncertain significance (Apr 12, 2023)
22-19355982-C-A			Benign (May 23, 2021)
22-19356222-T-C			Likely benign (May 21, 2018)
22-19356246-T-C		HIRA-related disorder	Benign (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C22orf39	protein_coding	protein_coding	ENST00000399562	3	96865

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000200	0.288	125302	0	393	125695	0.00156

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.204	78	73.1	1.07	0.00000400	877
Missense in Polyphen		23	22.9	1.0044		306
Synonymous	-0.674	34	29.4	1.16	0.00000149	266
Loss of Function	-0.0656	7	6.82	1.03	3.90e-7	73

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00810	0.00752
Ashkenazi Jewish	0.00175	0.00169
East Asian	0.0000580	0.0000544
Finnish	0.000389	0.000370
European (Non-Finnish)	0.00158	0.00147
Middle Eastern	0.0000580	0.0000544
South Asian	0.0000331	0.0000327
Other	0.00192	0.00180

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.148
• hipred: N
• hipred_score: 0.146
• ghis: 0.536

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: 2510002D24Rik
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Molecular function: protein binding