C1orf122

chromosome 1 open reading frame 122

Basic information

Region (hg38): 1:37806978-37809454

Links

ENSG00000197982 ∙ NCBI:127687 ∙ ∙ HGNC:24789 ∙ Uniprot:Q6ZSJ8 ∙ 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 C1orf122 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1orf122 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			18	20	2	40
Total	0	0	20	20	2

Variants in C1orf122

This is a list of pathogenic ClinVar variants found in the C1orf122 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-37806988-G-A			Benign (Jan 30, 2024)
1-37807105-G-A		not specified	Uncertain significance (Dec 13, 2023)
1-37807113-G-A			Likely benign (Dec 30, 2022)
1-37807131-C-T			Likely benign (Aug 27, 2023)
1-37807132-T-C		not specified	Uncertain significance (Nov 27, 2023)
1-37807138-G-A		not specified	Uncertain significance (Apr 25, 2023)
1-37807142-G-A		not specified	Uncertain significance (May 20, 2024)
1-37807148-T-C		YRDC-related disorder	Likely benign (Dec 21, 2022)
1-37807780-G-A			Likely benign (Apr 25, 2022)
1-37807817-G-A			Uncertain significance (Oct 10, 2022)
1-37807823-C-G			Uncertain significance (Jul 21, 2022)
1-37807824-G-A		YRDC-related disorder	Likely benign (Apr 16, 2023)
1-37807857-G-T		YRDC-related disorder	Likely benign (Feb 17, 2023)
1-37807880-C-G			Uncertain significance (Jun 22, 2022)
1-37807887-G-A		YRDC-related disorder	Likely benign (Dec 18, 2023)
1-37807891-G-A		not specified	Uncertain significance (Oct 26, 2022)
1-37807910-A-G		not specified	Uncertain significance (Mar 18, 2024)
1-37807930-G-A		Galloway-Mowat syndrome 10	Pathogenic (Nov 10, 2021)
1-37807935-C-T		YRDC-related disorder	Likely benign (Dec 20, 2022)
1-37807945-G-T		not specified	Uncertain significance (Sep 30, 2022)
1-37807963-G-T		not specified	Uncertain significance (Jul 25, 2023)
1-37807971-C-G		YRDC-related disorder	Likely benign (Jul 06, 2022)
1-37807972-A-G		not specified	Uncertain significance (Jan 06, 2023)
1-37808004-C-T		YRDC-related disorder	Likely benign (Sep 22, 2022)
1-37808010-C-T			Likely benign (Jun 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1orf122	protein_coding	protein_coding	ENST00000373042	3	2476

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.143	0.643	124115	0	11	124126	0.0000443

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.428	27	34.0	0.793	0.00000159	665
Missense in Polyphen		6	4.4956	1.3346		48
Synonymous	1.46	9	16.6	0.543	7.56e-7	251
Loss of Function	0.629	1	1.95	0.514	8.32e-8	56

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000892	0.00000892
Middle Eastern	0.0000544	0.0000544
South Asian	0.000294	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0582

Haploinsufficiency Scores

• pHI: 0.0895
• hipred: N
• hipred_score: 0.327
• ghis: 0.393

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: 1110065P20Rik