C1D

protein-coding

C1D nuclear receptor corepressor

Gene summary

The protein encoded by this gene is a DNA binding and apoptosis-inducing protein and is localized in the nucleus. It is also a Rac3-interacting protein which acts as a corepressor for the thyroid hormone receptor. This protein is thought to regulate TRAX/Translin complex formation. Alternate splicing results in multiple transcript variants that encode the same protein. Multiple pseudogenes of this gene are found on chromosome 10.[provided by RefSeq, Jun 2010]

MANE transcript

NM_173177.3

Inheritance

—

ClinVar variants

U:19B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr2:68,041,130-68,110,948

External References & Databases

Ensembl (ENSG00000197223)

Transcript & Mutation Effects

hg38 • Region Span ~69.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to C1D variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 17

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173177.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar		1 clinvar	2
missense			18 clinvar			18
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	19	0	1	20

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 74 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173177.3	RefSeq	NP_775269.1	4	MANE Select
ENST00000410067.8	Ensembl	ENSP00000386468.3	4	MANE Select
NM_001190263.2	RefSeq	NP_001177192.1	4	Standard
NM_001190265.2	RefSeq	NP_001177194.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

RNA degradation - Homo sapiens (human)

Biological Process

maturation of 5.8S rRNA
rRNA processing
apoptotic process
negative regulation of transcription, DNA-templated

Molecular Function

DNA binding
transcription corepressor activity
RNA binding
protein binding
nuclear receptor binding

Cellular Component

nuclear exosome (RNase complex)
nucleus
nucleoplasm
nucleolus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000355848
Coding exons: 4
Length: 69819
Individuals with no LoFs: 125671
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125700
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.00307	65	64.9	1.00	0.00000296	918
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000066	0.000058	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00076	0.00076	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00010	0.000097	rare
South Asian	0.000038	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.766

Intolerance Scores

LoFtool: 0.954
RVIS EVS: 0.15
RVIS percentile EVS: 64.11

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): H
Indispensability pred.: N
Indispensability score: 0.184

Gene Damage Prediction

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