CCDC12

coiled-coil domain containing 12, the group of Spliceosomal Bact complex|Spliceosomal P complex|Spliceosomal C complex

Basic information

Region (hg38): 3:46921725-46982010

Links

ENSG00000160799 ∙ NCBI:151903 ∙ ∙ HGNC:28332 ∙ Uniprot:Q8WUD4 ∙ 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 CCDC12 gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC12 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			5			5
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	6	0	0

Variants in CCDC12

This is a list of pathogenic ClinVar variants found in the CCDC12 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-46922071-A-G		not specified	Uncertain significance (Mar 21, 2023)
3-46922297-A-T		not specified	Uncertain significance (Sep 12, 2023)
3-46923616-G-C		not specified	Uncertain significance (Mar 17, 2023)
3-46923627-C-T		not specified	Uncertain significance (Jan 10, 2022)
3-46925534-C-G		not specified	Uncertain significance (Oct 26, 2022)
3-46976699-C-G		not specified	Uncertain significance (Nov 13, 2023)
3-46976723-T-C		not specified	Likely benign (Feb 05, 2024)
3-46976725-G-A		not specified	Uncertain significance (Feb 06, 2023)
3-46976732-T-A		not specified	Uncertain significance (Sep 29, 2022)
3-46976753-C-G		not specified	Uncertain significance (Aug 26, 2022)
3-46979345-A-T			Benign (Jun 19, 2021)
3-46979533-A-G			Benign (Jun 19, 2021)
3-46979634-A-G			Benign (Jun 19, 2021)
3-46979684-G-A		Gray platelet syndrome	Uncertain significance (Jan 13, 2018)
3-46979700-C-T		Gray platelet syndrome	Uncertain significance (Jan 12, 2018)
3-46979742-C-G		Gray platelet syndrome	Uncertain significance (Apr 06, 2018)
3-46979786-G-A		Gray platelet syndrome	Uncertain significance (Jan 13, 2018)
3-46979842-G-GGCCGGA		Gray platelet syndrome	Uncertain significance (Jun 14, 2016)
3-46979898-C-T		Gray platelet syndrome	Uncertain significance (Oct 09, 2023)
3-46979900-C-T			Likely benign (Jun 15, 2018)
3-46979923-C-T		Gray platelet syndrome	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC12	protein_coding	protein_coding	ENST00000425441	7	60285

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0401	0.933	125508	2	238	125748	0.000955

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.418	89	101	0.883	0.00000555	1136
Missense in Polyphen		25	32.794	0.76234		371
Synonymous	-0.120	43	42.0	1.02	0.00000249	336
Loss of Function	1.91	4	10.8	0.371	5.56e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0171	0.0134
Ashkenazi Jewish	0.00	0.00
East Asian	0.000134	0.000109
Finnish	0.0000523	0.0000462
European (Non-Finnish)	0.0000504	0.0000439
Middle Eastern	0.000134	0.000109
South Asian	0.000158	0.000131
Other	0.000187	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Spliceosome - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.197
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.49

Haploinsufficiency Scores

• pHI: 0.0857
• hipred: Y
• hipred_score: 0.739
• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.583

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc12

Gene ontology

• Molecular function: protein binding