CCHCR1

protein-coding

coiled-coil alpha-helical rod protein 1

Gene summary

This gene encodes a protein with five coiled-coil alpha-helical rod domains that is thought to act as a regulator of mRNA metabolism through its interaction with mRNA-decapping protein 4. It localizes to P-bodies, the site of mRNA metabolism, with an N-terminus that is required for this subcellular localization, suggesting it is a P-body component. Naturally occurring mutations in this gene are associated with psoriasis. [provided by RefSeq, May 2017]

Previous symbols:

C6orf18

MANE transcript

NM_001105564.2

Inheritance

—

ClinVar variants

U:125B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr6:31,142,439-31,158,238

External References & Databases

Ensembl (ENSG00000204536)

Transcript & Mutation Effects

hg38 • Region Span ~15.8 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 CCHCR1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 109

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001105564.2. 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			2 clinvar	1 clinvar		3
missense			115 clinvar	8 clinvar	1 clinvar	124
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	125	9	1	135

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 52 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001105564.2	RefSeq	NP_001099034.1	18	MANE Select
ENST00000396268.8	Ensembl	ENSP00000379566.3	18	MANE Select
NM_001105563.3	RefSeq	NP_001099033.1	18	Standard
NM_001394641.1	RefSeq	NP_001381570.1	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein export from nucleus
multicellular organism development
cell differentiation

Cellular Component

nucleus
centriole
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396268
Coding exons: 18
Length: 15800
Individuals with no LoFs: 125175
Homozygous LoFs: 2
Heterozygous LoFs: 570
Defined: 125747
p: 0.00228

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.91	384	504	0.761	0.0000302	5535
Missense (PolyPhen)		128	159.71	0.80147		1744
Synonymous	3.01	143	197	0.727	0.0000101	1790
Loss of Function	2.43	34	53.1	0.640	0.00000283	533

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0012	0.0012	notable
Latino/Admixed American	0.0020	0.0020	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0.00086	0.00074	rare
European (Non-Finnish)	0.0036	0.0035	notable
South Asian	0.0019	0.0018	notable
Other	0.0018	0.0018	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be a regulator of keratinocyte proliferation or differentiation.;

Intolerance Scores

LoFtool: 0.990
RVIS EVS: 3.54
RVIS percentile EVS: 99.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.637

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High