CCDC112

coiled-coil domain containing 112

Basic information

Region (hg38): 5:115267190-115296693

Links

ENSG00000164221 ∙ NCBI:153733 ∙ ∙ HGNC:28599 ∙ Uniprot:Q8NEF3 ∙ 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 CCDC112 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC112 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					4	4
missense			40	3	1	44
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	3	5

Variants in CCDC112

This is a list of pathogenic ClinVar variants found in the CCDC112 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-115268892-T-C		not specified	Uncertain significance (Dec 07, 2024)
5-115268894-T-C		not specified	Uncertain significance (May 02, 2023)
5-115268898-G-C		not specified	Uncertain significance (Aug 05, 2024)
5-115268909-G-C		not specified	Uncertain significance (Dec 18, 2023)
5-115269707-T-A		not specified	Uncertain significance (Mar 08, 2025)
5-115269768-C-T		not specified	Uncertain significance (Sep 27, 2021)
5-115269771-G-T		not specified	Uncertain significance (Jun 23, 2023)
5-115269792-G-T		not specified	Uncertain significance (Jul 09, 2021)
5-115269797-T-A		not specified	Uncertain significance (Jul 27, 2024)
5-115271234-T-A		not specified	Uncertain significance (Oct 26, 2021)
5-115271245-C-G		not specified	Uncertain significance (Jan 27, 2025)
5-115271342-T-C			Benign (Dec 31, 2019)
5-115271367-C-A		not specified	Uncertain significance (Mar 01, 2024)
5-115271373-C-T		not specified	Uncertain significance (Feb 21, 2024)
5-115271395-C-G		not specified	Uncertain significance (Aug 05, 2024)
5-115271416-A-T		not specified	Uncertain significance (Apr 19, 2024)
5-115271434-T-C		not specified	Uncertain significance (Jan 23, 2023)
5-115271437-A-G		not specified	Uncertain significance (Aug 08, 2022)
5-115271455-G-T		not specified	Uncertain significance (Jan 16, 2025)
5-115271532-T-C		not specified	Uncertain significance (Jun 05, 2023)
5-115271545-C-T		not specified	Likely benign (Jun 21, 2021)
5-115271548-G-A		not specified	Uncertain significance (Jun 05, 2024)
5-115271589-C-T		not specified	Likely benign (Feb 27, 2023)
5-115271595-T-C			Benign (Dec 26, 2018)
5-115275236-G-C		not specified	Uncertain significance (Jun 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC112	protein_coding	protein_coding	ENST00000379611	10	29644

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.849	0.151	125712	0	20	125732	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.114	256	251	1.02	0.0000114	3513
Missense in Polyphen		51	57.601	0.8854		908
Synonymous	-0.0415	83	82.5	1.01	0.00000362	886
Loss of Function	4.05	5	28.2	0.177	0.00000137	376

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000974	0.0000932
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000145	0.000132
Middle Eastern	0.00	0.00
South Asian	0.0000334	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0990

Intolerance Scores

• loftool: 0.681
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• pHI: 0.269
• hipred: Y
• hipred_score: 0.518
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.922

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc112

Gene ontology

• Molecular function: protein binding