CHAF1B

chromatin assembly factor 1 subunit B, the group of WD repeat domain containing

Basic information

Region (hg38): 21:36385391-36419015

Links

ENSG00000159259 ∙ NCBI:8208 ∙ OMIM:601245 ∙ HGNC:1911 ∙ Uniprot:Q13112 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHAF1B gene.

• Inborn genetic diseases (20 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHAF1B 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				2	1	3
missense			18	3	3	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	5	4

Variants in CHAF1B

This is a list of pathogenic ClinVar variants found in the CHAF1B region.

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

Position	Type	Phenotype	Significance	ClinVar
21-36386183-T-C			Likely benign (Apr 01, 2024)
21-36386260-A-G		not specified	Uncertain significance (Jun 16, 2023)
21-36387629-A-G		not specified	Uncertain significance (Dec 08, 2023)
21-36387668-C-G		not specified	Uncertain significance (Jun 28, 2022)
21-36387673-G-T		not specified	Uncertain significance (Jul 09, 2021)
21-36387676-G-A		not specified	Uncertain significance (May 24, 2023)
21-36387698-C-T		not specified	Uncertain significance (May 05, 2023)
21-36394641-G-A		not specified	Uncertain significance (Oct 25, 2022)
21-36397429-A-G		Global developmental delay;Intellectual disability;Attention deficit hyperactivity disorder	Likely pathogenic (Dec 01, 2014)
21-36399525-C-A		not specified	Uncertain significance (Jan 10, 2022)
21-36399537-A-C		not specified	Uncertain significance (Jun 05, 2023)
21-36399571-C-T		not specified	Uncertain significance (Jan 04, 2022)
21-36399598-A-G		not specified	Uncertain significance (Dec 06, 2022)
21-36402827-G-A		not specified	Uncertain significance (Aug 12, 2021)
21-36409408-A-G		Malignant tumor of prostate	Uncertain significance (-)
21-36409420-C-T		not specified	Uncertain significance (Apr 07, 2022)
21-36411465-G-A		not specified	Uncertain significance (Oct 05, 2023)
21-36411494-G-A			Likely benign (Apr 01, 2023)
21-36411522-G-A		not specified	Uncertain significance (Nov 15, 2021)
21-36412996-A-G		not specified	Likely benign (Dec 28, 2022)
21-36413033-A-G		not specified	Uncertain significance (Dec 15, 2023)
21-36413051-C-T		not specified	Uncertain significance (Dec 21, 2023)
21-36413066-C-T			Benign (Dec 31, 2019)
21-36413102-C-T		not specified	Uncertain significance (Mar 06, 2023)
21-36413280-G-A			Benign (Jan 30, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHAF1B	protein_coding	protein_coding	ENST00000314103	13	33638

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.428	0.572	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.82	240	333	0.720	0.0000191	3634
Missense in Polyphen		48	109.18	0.43966		1181
Synonymous	0.439	129	136	0.952	0.00000896	1120
Loss of Function	3.77	6	27.2	0.220	0.00000131	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000124
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000573	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000573	0.0000544
South Asian	0.00	0.00
Other	0.000173	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Complex that is 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. {ECO:0000269|PubMed:9813080}.
• Pathway: btg family proteins and cell cycle regulation (Consensus)

Recessive Scores

• pRec: 0.0832

Intolerance Scores

• loftool: 0.333
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.44

Haploinsufficiency Scores

• pHI: 0.666
• hipred: Y
• hipred_score: 0.773
• ghis: 0.457

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.964

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chaf1b

Zebrafish Information Network

• Gene name: chaf1b
• Affected structure: retinal ganglion cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: DNA replication;DNA repair;nucleosome assembly;DNA replication-dependent nucleosome assembly;cell cycle;chromatin assembly
• Cellular component: nuclear chromatin;nucleus;nucleoplasm;cytoplasm;cytosol;protein-containing complex;CAF-1 complex
• Molecular function: chromatin binding;protein binding;histone binding;unfolded protein binding