C1D

C1D nuclear receptor corepressor

Basic information

Region (hg38): 2:68041130-68110948

Links

ENSG00000197223 ∙ NCBI:10438 ∙ OMIM:606997 ∙ HGNC:29911 ∙ Uniprot:Q13901 ∙ 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 C1D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1D 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	1
missense			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	1

Variants in C1D

This is a list of pathogenic ClinVar variants found in the C1D region.

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

Position	Type	Phenotype	Significance	ClinVar
2-68042917-A-C		not specified	Uncertain significance (May 11, 2022)
2-68042951-G-A		not specified	Uncertain significance (Dec 19, 2023)
2-68042959-T-C		not specified	Uncertain significance (May 06, 2024)
2-68042966-A-G		not specified	Uncertain significance (Jan 09, 2024)
2-68046346-C-A		not specified	Uncertain significance (Feb 11, 2022)
2-68047206-C-G		not specified	Uncertain significance (Dec 18, 2023)
2-68047299-T-C			Benign (Apr 16, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1D	protein_coding	protein_coding	ENST00000355848	4	69819

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0341	0.835	125671	0	29	125700	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00307	65	64.9	1.00	0.00000296	918
Missense in Polyphen		8	10.529	0.75979		171
Synonymous	-0.710	27	22.7	1.19	0.00000117	243
Loss of Function	1.20	3	6.23	0.482	2.59e-7	98

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000658	0.0000658
Ashkenazi Jewish	0.000104	0.0000992
East Asian	0.000764	0.000761
Finnish	0.00	0.00
European (Non-Finnish)	0.000101	0.0000967
Middle Eastern	0.000764	0.000761
South Asian	0.0000380	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the recruitment of the RNA exosome complex to pre-rRNA to mediate the 3'-5' end processing of the 5.8S rRNA; this function may include MPHOSPH6. Can activate PRKDC not only in the presence of linear DNA but also in the presence of supercoiled DNA. Can induce apoptosis in a p53/TP53 dependent manner. May regulate the TRAX/TSN complex formation. Potentiates transcriptional repression by NR1D1 and THRB (By similarity). {ECO:0000250, ECO:0000269|PubMed:10362552, ECO:0000269|PubMed:11801738, ECO:0000269|PubMed:17412707, ECO:0000269|PubMed:9679063}.
• Pathway: RNA degradation - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.766

Intolerance Scores

• loftool: 0.954
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.11

Haploinsufficiency Scores

• pHI: 0.654
• hipred: Y
• hipred_score: 0.633
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.184

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C1d

Gene ontology

• Biological process: maturation of 5.8S rRNA;rRNA processing;apoptotic process;negative regulation of transcription, DNA-templated
• Cellular component: nuclear exosome (RNase complex);nucleus;nucleoplasm;nucleolus;cytoplasm;transcriptional repressor complex
• Molecular function: DNA binding;transcription corepressor activity;RNA binding;protein binding;nuclear receptor binding