CC2D1B

coiled-coil and C2 domain containing 1B, the group of C2 domain containing

Basic information

Region (hg38): 1:52345723-52366205

Links

ENSG00000154222 ∙ NCBI:200014 ∙ ∙ HGNC:29386 ∙ Uniprot:Q5T0F9 ∙ 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 CC2D1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CC2D1B 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				1	3	4
missense			69	4		73
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	69	5	3

Variants in CC2D1B

This is a list of pathogenic ClinVar variants found in the CC2D1B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-52346108-A-G		not specified	Uncertain significance (May 29, 2024)
1-52346131-G-T		not specified	Uncertain significance (Sep 22, 2022)
1-52346154-C-T		not specified	Uncertain significance (Nov 21, 2022)
1-52346163-T-C		not specified	Uncertain significance (Jul 22, 2024)
1-52353523-A-G		not specified	Uncertain significance (Nov 14, 2024)
1-52353569-C-T		not specified	Likely benign (May 02, 2024)
1-52353623-C-G		not specified	Uncertain significance (Aug 10, 2023)
1-52354631-A-G		not specified	Uncertain significance (Apr 24, 2024)
1-52354634-C-T		not specified	Uncertain significance (Oct 02, 2023)
1-52354640-C-G		not specified	Uncertain significance (Nov 20, 2023)
1-52354645-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-52354668-G-A			Benign (Nov 24, 2017)
1-52354678-T-C		not specified	Uncertain significance (Nov 26, 2024)
1-52354860-C-A		not specified	Uncertain significance (Oct 03, 2023)
1-52354895-C-T		not specified	Uncertain significance (Nov 11, 2024)
1-52354897-C-T		not specified	Uncertain significance (Feb 23, 2023)
1-52354909-T-C		not specified	Uncertain significance (Jul 19, 2023)
1-52354925-A-C		not specified	Uncertain significance (Feb 08, 2023)
1-52355443-C-G		not specified	Uncertain significance (Jan 20, 2023)
1-52355633-C-T		not specified	Uncertain significance (Nov 15, 2024)
1-52355634-G-A		not specified	Uncertain significance (Jun 29, 2023)
1-52355638-A-T		not specified	Uncertain significance (Oct 29, 2024)
1-52355655-C-T		not specified	Uncertain significance (Nov 04, 2023)
1-52355774-G-A		not specified	Uncertain significance (May 14, 2024)
1-52355814-C-G		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CC2D1B	protein_coding	protein_coding	ENST00000371586	23	20471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.75e-18	0.719	125577	0	171	125748	0.000680

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.01	570	506	1.13	0.0000305	5479
Missense in Polyphen		187	156.25	1.1968		1725
Synonymous	0.560	193	203	0.950	0.0000121	1768
Loss of Function	2.04	36	51.8	0.694	0.00000304	547

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00182	0.00178
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.00132	0.00131
Finnish	0.000427	0.000416
European (Non-Finnish)	0.000541	0.000528
Middle Eastern	0.00132	0.00131
South Asian	0.000900	0.000882
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that binds specifically to the DRE (dual repressor element) and represses HTR1A gene transcription in neuronal cells. {ECO:0000269|PubMed:19423080}.

Intolerance Scores

• loftool: 0.877
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.29

Haploinsufficiency Scores

• pHI: 0.0959
• hipred: N
• hipred_score: 0.443
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.627

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cc2d1b
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;intracellular membrane-bounded organelle
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription repressor activity, RNA polymerase II-specific;protein binding