CHAF1A

chromatin assembly factor 1 subunit A

Basic information

Region (hg38): 19:4402640-4445018

Links

ENSG00000167670 ∙ NCBI:10036 ∙ OMIM:601246 ∙ HGNC:1910 ∙ Uniprot:Q13111 ∙ 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 CHAF1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHAF1A 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					1	1
missense			57	6		63
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	57	7	1

Variants in CHAF1A

This is a list of pathogenic ClinVar variants found in the CHAF1A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-4402793-G-A		not specified	Uncertain significance (Aug 12, 2021)
19-4402800-G-A		not specified	Uncertain significance (Jan 29, 2024)
19-4408950-G-A		not specified	Uncertain significance (Nov 15, 2021)
19-4409007-G-A		not specified	Likely benign (Oct 26, 2022)
19-4409008-C-T		not specified	Uncertain significance (Apr 08, 2022)
19-4409009-C-G			Benign (Nov 14, 2018)
19-4409083-A-T		not specified	Uncertain significance (May 16, 2022)
19-4409118-G-A		not specified	Likely benign (Jan 04, 2022)
19-4409128-T-C		not specified	Uncertain significance (Jan 17, 2024)
19-4409167-C-T		not specified	Uncertain significance (Nov 18, 2022)
19-4409187-C-T		not specified	Uncertain significance (Jun 09, 2022)
19-4409251-G-A		not specified	Uncertain significance (Feb 28, 2024)
19-4409263-G-C		not specified	Uncertain significance (Jun 07, 2024)
19-4409322-A-G		not specified	Uncertain significance (Jun 27, 2023)
19-4409412-C-T		not specified	Uncertain significance (Jul 14, 2021)
19-4409428-T-C		not specified	Uncertain significance (Feb 28, 2024)
19-4409499-A-G		not specified	Uncertain significance (Mar 01, 2023)
19-4409521-T-G		not specified	Uncertain significance (Nov 18, 2022)
19-4409538-G-C		not specified	Uncertain significance (Mar 03, 2022)
19-4409551-C-G		not specified	Uncertain significance (Dec 20, 2023)
19-4409592-A-G		not specified	Likely benign (Dec 17, 2023)
19-4409604-A-G		not specified	Uncertain significance (Oct 25, 2023)
19-4409655-T-G		not specified	Uncertain significance (Dec 28, 2023)
19-4409695-C-T		not specified	Uncertain significance (Jan 24, 2024)
19-4409737-C-T		not specified	Uncertain significance (May 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHAF1A	protein_coding	protein_coding	ENST00000301280	15	42357

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000284	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	458	584	0.785	0.0000373	6282
Missense in Polyphen		94	166.82	0.56347		1743
Synonymous	-0.909	269	251	1.07	0.0000180	1839
Loss of Function	5.72	1	40.1	0.0249	0.00000189	509

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000268	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Core component of the CAF-1 complex, a complex thought to mediate chromatin assembly in DNA replication and DNA repair. Assembles histone octamers onto replicating DNA in vitro. CAF-1 performs the first step of the nucleosome assembly process, bringing newly synthesized histones H3 and H4 to replicating DNA; histones H2A/H2B can bind to this chromatin precursor subsequent to DNA replication to complete the histone octamer. CHAF1A binds to histones H3 and H4. It may play a role in heterochromatin maintenance in proliferating cells by bringing newly synthesized cbx proteins to heterochromatic DNA replication foci (By similarity). {ECO:0000250, ECO:0000269|PubMed:15327775}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;Nanoparticle triggered autophagic cell death;btg family proteins and cell cycle regulation (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.126
• rvis_EVS: 0.32
• rvis_percentile_EVS: 72.85

Haploinsufficiency Scores

• pHI: 0.925
• hipred: Y
• hipred_score: 0.734
• ghis: 0.574

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.972

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chaf1a
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cellular phenotype

Gene ontology

• Biological process: DNA replication;DNA repair;nucleosome assembly;DNA replication-dependent nucleosome assembly;cell cycle;chromatin assembly
• Cellular component: nuclear chromatin;nucleus;protein-containing complex;CAF-1 complex
• Molecular function: chromatin binding;protein binding;identical protein binding;unfolded protein binding;chromo shadow domain binding