C3orf22

chromosome 3 open reading frame 22

Basic information

Region (hg38): 3:126526999-126558965

Links

ENSG00000180697 ∙ NCBI:152065 ∙ ∙ HGNC:28534 ∙ Uniprot:Q8N5N4 ∙ 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 C3orf22 gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C3orf22 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)						0
splice region						0
non coding			15			15
Total	0	0	15	0	0

Variants in C3orf22

This is a list of pathogenic ClinVar variants found in the C3orf22 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-126536323-C-G		not specified	Uncertain significance (Mar 28, 2022)
3-126536336-C-T		not specified	Uncertain significance (Feb 08, 2025)
3-126541737-C-T		not specified	Uncertain significance (Aug 21, 2024)
3-126541767-A-G		not specified	Uncertain significance (Jan 31, 2023)
3-126541842-G-T		not specified	Uncertain significance (Mar 19, 2024)
3-126541846-C-G		not specified	Uncertain significance (Jun 29, 2023)
3-126541887-T-A		not specified	Uncertain significance (Apr 04, 2024)
3-126541905-C-T		not specified	Uncertain significance (Jan 22, 2025)
3-126541929-C-A		not specified	Uncertain significance (May 14, 2024)
3-126541937-G-A		not specified	Uncertain significance (Jan 31, 2023)
3-126541937-G-C		not specified	Uncertain significance (Apr 18, 2024)
3-126541959-G-C		not specified	Uncertain significance (Mar 16, 2022)
3-126541959-G-T		not specified	Uncertain significance (Dec 12, 2024)
3-126542035-C-A		not specified	Uncertain significance (Jan 26, 2022)
3-126542120-C-G		not specified	Uncertain significance (Nov 12, 2021)
3-126542124-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-126542129-A-T		not specified	Uncertain significance (Feb 07, 2025)
3-126542148-G-A		not specified	Uncertain significance (Dec 14, 2023)
3-126542156-G-C		not specified	Uncertain significance (Nov 18, 2022)
3-126542160-G-T		not specified	Uncertain significance (Sep 26, 2024)
3-126542175-T-G		not specified	Uncertain significance (Nov 03, 2023)
3-126542184-G-A		not specified	Uncertain significance (Dec 12, 2023)
3-126542186-G-T		not specified	Uncertain significance (Feb 24, 2025)
3-126542213-C-T		not specified	Uncertain significance (Jun 26, 2024)
3-126542215-C-A		not specified	Uncertain significance (Dec 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C3orf22	protein_coding	protein_coding	ENST00000318225	3	31967

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.100	0.783	125676	0	3	125679	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0378	87	86.0	1.01	0.00000518	894
Missense in Polyphen		21	29.109	0.72143		263
Synonymous	0.0988	40	40.8	0.980	0.00000270	302
Loss of Function	1.21	2	4.87	0.411	2.08e-7	51

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.0108
• hipred: N
• hipred_score: 0.153
• ghis: 0.465

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: BC048671