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

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.

• not_specified (25 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. These statistics are base on transcript: NM_001277074.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			22	1		23
nonsense						0
start loss			2			2
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	24	1	0

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