CHCT1

CHD1 helical C-terminal domain containing 1

Basic information

Region (hg38): 17:60392428-60431426

Previous symbols: [ "C17orf64" ]

Links

ENSG00000141371

∙ NCBI:124773 ∙ ∙ HGNC:26990 ∙ Uniprot:Q86WR6 ∙ 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 CHCT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHCT1 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHCT1	protein_coding	protein_coding	ENST00000269127	6	38993

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.56e-12	0.00780	125717	0	18	125735	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.686	108	130	0.831	0.00000717	1524
Missense in Polyphen		20	34.794	0.57482		472
Synonymous	0.0324	54	54.3	0.994	0.00000320	433
Loss of Function	-0.952	16	12.4	1.29	6.96e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000643	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000658	0.000653
Finnish	0.0000536	0.0000462
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.000658	0.000653
South Asian	0.0000672	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

loftool: 0.358
rvis_EVS: 0.37
rvis_percentile_EVS: 75.12

Haploinsufficiency Scores

pHI: 0.143
hipred: N
hipred_score: 0.123
ghis: 0.432

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: 1700125H20Rik
Phenotype: normal phenotype;