CHRAC1

chromatin accessibility complex subunit 1, the group of Chromatin accessibility complex

Basic information

Region (hg38): 8:140511311-140517154

Links

ENSG00000104472 ∙ NCBI:54108 ∙ OMIM:607268 ∙ HGNC:13544 ∙ Uniprot:Q9NRG0 ∙ 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 CHRAC1 gene.

• not_specified (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHRAC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017444.6. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			14	1		15
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	14	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHRAC1	protein_coding	protein_coding	ENST00000220913	3	5840

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0695	0.751	114742	0	2	114744	0.00000872

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.349	50	57.4	0.871	0.00000256	842
Missense in Polyphen		13	16.965	0.76627		253
Synonymous	0.479	20	22.9	0.873	0.00000110	233
Loss of Function	0.928	2	4.00	0.499	1.67e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000936	0.00000925
Middle Eastern	0.00	0.00
South Asian	0.0000395	0.0000376
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Forms a complex with DNA polymerase epsilon subunit POLE3 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome remodeling activity of ISWI/SNF2H and ACF1.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.561
• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.89

Haploinsufficiency Scores

• pHI: 0.153
• hipred: Y
• hipred_score: 0.705
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.961

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chrac1

Zebrafish Information Network

• Gene name: chrac1
• Affected structure: primitive erythrocyte differentiation
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: chromatin remodeling;heterochromatin organization involved in chromatin silencing;DNA biosynthetic process
• Cellular component: epsilon DNA polymerase complex;CHRAC
• Molecular function: DNA binding;DNA-directed DNA polymerase activity;protein binding;protein heterodimerization activity