CCDC122

coiled-coil domain containing 122

Basic information

Region (hg38): 13:43823909-43879740

Links

ENSG00000151773 ∙ NCBI:160857 ∙ OMIM:613408 ∙ HGNC:26478 ∙ Uniprot:Q5T0U0 ∙ 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 CCDC122 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC122 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in CCDC122

This is a list of pathogenic ClinVar variants found in the CCDC122 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-43837346-T-G		not specified	Uncertain significance (Apr 18, 2023)
13-43837356-C-G		not specified	Uncertain significance (Nov 20, 2023)
13-43859494-C-A		Leprosy, susceptibility to, 1	Uncertain risk allele (Jun 10, 2022)
13-43859737-T-C		not specified	Uncertain significance (Feb 22, 2023)
13-43859853-T-C		not specified	Uncertain significance (Jan 16, 2024)
13-43859892-T-C		not specified	Uncertain significance (Dec 16, 2021)
13-43859899-C-T		not specified	Uncertain significance (Apr 12, 2023)
13-43868716-T-C		not specified	Uncertain significance (Apr 12, 2024)
13-43868752-T-G		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC122	protein_coding	protein_coding	ENST00000444614	5	55783

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000378	0.605	125694	0	10	125704	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.116	122	118	1.03	0.00000546	1818
Missense in Polyphen		33	30.978	1.0653		497
Synonymous	0.857	31	37.7	0.822	0.00000171	431
Loss of Function	0.905	10	13.6	0.735	8.30e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000118	0.000118
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000342	0.0000327
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0943

Intolerance Scores

• loftool: 0.807
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.98

Haploinsufficiency Scores

• pHI: 0.248
• hipred: N
• hipred_score: 0.190
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.308

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ccdc122
• Phenotype: skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype