CCHCR1

coiled-coil alpha-helical rod protein 1

Basic information

Region (hg38): 6:31142438-31158238

Previous symbols: [ "C6orf18" ]

Links

ENSG00000204536 ∙ NCBI:54535 ∙ OMIM:605310 ∙ HGNC:13930 ∙ Uniprot:Q8TD31 ∙ 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 CCHCR1 gene.

• Inborn genetic diseases (32 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCHCR1 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						0
missense			27	4	4	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	28	4	4

Variants in CCHCR1

This is a list of pathogenic ClinVar variants found in the CCHCR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31142635-T-C		not specified	Uncertain significance (Feb 22, 2023)
6-31142638-T-C		not specified	Uncertain significance (Jun 30, 2022)
6-31143103-C-T		not specified	Likely benign (Feb 06, 2024)
6-31143299-C-T		not specified	Uncertain significance (Jun 21, 2021)
6-31143300-G-A		not specified	Uncertain significance (Mar 23, 2023)
6-31143311-C-T		not specified	Uncertain significance (Aug 22, 2022)
6-31143322-C-G		not specified	Uncertain significance (Jul 20, 2022)
6-31143329-C-T		not specified	Uncertain significance (Mar 23, 2022)
6-31143401-C-T		not specified	Uncertain significance (Nov 12, 2021)
6-31144729-C-T		not specified	Uncertain significance (Dec 20, 2023)
6-31144740-A-G		not specified	Uncertain significance (Jul 08, 2021)
6-31144756-G-A		not specified	Uncertain significance (Dec 21, 2022)
6-31144756-G-C		not specified	Uncertain significance (May 27, 2022)
6-31144891-C-G		not specified	Likely benign (Apr 05, 2023)
6-31144960-C-A			Benign (Jul 13, 2018)
6-31144966-G-A		not specified	Uncertain significance (Mar 16, 2022)
6-31145205-G-A		not specified	Uncertain significance (Feb 05, 2024)
6-31145249-C-T		not specified	Uncertain significance (Jun 27, 2022)
6-31145470-G-A		not specified	Uncertain significance (Sep 28, 2022)
6-31145734-C-T		not specified	Uncertain significance (Oct 27, 2021)
6-31145737-T-C		not specified	Likely benign (May 17, 2023)
6-31148447-G-A		not specified	Uncertain significance (Oct 04, 2022)
6-31148650-C-T		not specified	Uncertain significance (Oct 27, 2022)
6-31148653-C-A		not specified	Uncertain significance (Jan 19, 2024)
6-31148671-G-C		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCHCR1	protein_coding	protein_coding	ENST00000396268	18	15800

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.01e-16	0.959	125175	2	570	125747	0.00228

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.91	384	504	0.761	0.0000302	5535
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00326	0.00318
Ashkenazi Jewish	0.00	0.00
East Asian	0.000328	0.000326
Finnish	0.000859	0.000739
European (Non-Finnish)	0.00363	0.00349
Middle Eastern	0.000328	0.000326
South Asian	0.00187	0.00180
Other	0.00185	0.00179

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0866
• hipred: N
• hipred_score: 0.478
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.637

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cchcr1

Gene ontology

• Biological process: protein export from nucleus;multicellular organism development;cell differentiation
• Cellular component: nucleus;centriole;cytosol