CCDC12

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

Basic information

Region (hg38): 3:46916634-46982010

Links

ENSG00000160799NCBI:151903HGNC:28332Uniprot:Q8WUD4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC12 gene.

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
7
clinvar
1
clinvar
8
nonsense
0
start loss
1
clinvar
1
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 8 1 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)2527783
3-46922265-C-T not specified Uncertain significance (Mar 25, 2024)3263800
3-46922297-A-T not specified Uncertain significance (Sep 12, 2023)2622833
3-46923616-G-C not specified Uncertain significance (Mar 17, 2023)2526208
3-46923627-C-T not specified Uncertain significance (Jan 10, 2022)3138286
3-46925534-C-G not specified Uncertain significance (Oct 26, 2022)2391042
3-46976699-C-G not specified Uncertain significance (Nov 13, 2023)3138288
3-46976723-T-C not specified Likely benign (Feb 05, 2024)3138287
3-46976725-G-A not specified Uncertain significance (Feb 06, 2023)2481164
3-46976732-T-A not specified Uncertain significance (Sep 29, 2022)2314490
3-46976753-C-G not specified Uncertain significance (Aug 26, 2022)2309190
3-46979345-A-T Benign (Jun 19, 2021)1288588
3-46979533-A-G Benign (Jun 19, 2021)1251507
3-46979634-A-G Benign (Jun 19, 2021)1248264
3-46979684-G-A Gray platelet syndrome Uncertain significance (Jan 13, 2018)899579
3-46979700-C-T Gray platelet syndrome Uncertain significance (Jan 12, 2018)345608
3-46979742-C-G Gray platelet syndrome Uncertain significance (Apr 06, 2018)899580
3-46979786-G-A Gray platelet syndrome Uncertain significance (Jan 13, 2018)345609
3-46979842-G-GGCCGGA Gray platelet syndrome Uncertain significance (Jun 14, 2016)345610
3-46979898-C-T Gray platelet syndrome Uncertain significance (Oct 09, 2023)2582769
3-46979900-C-T Likely benign (Jun 15, 2018)753173
3-46979923-C-T Gray platelet syndrome Uncertain significance (Jan 13, 2018)345611

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CCDC12protein_codingprotein_codingENST00000425441 760285
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.04010.93312550822381257480.000955
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.418891010.8830.000005551136
Missense in Polyphen2532.7940.76234371
Synonymous-0.1204342.01.020.00000249336
Loss of Function1.91410.80.3715.56e-7136

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.01710.0134
Ashkenazi Jewish0.000.00
East Asian0.0001340.000109
Finnish0.00005230.0000462
European (Non-Finnish)0.00005040.0000439
Middle Eastern0.0001340.000109
South Asian0.0001580.000131
Other0.0001870.000163

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
essential_gene_gene_trap
gene_indispensability_pred
E
gene_indispensability_score
0.583

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ccdc12
Phenotype

Gene ontology

Biological process
Cellular component
Molecular function
protein binding