ASF1A

anti-silencing function 1A histone chaperone

Basic information

Region (hg38): 6:118894152-118909171

Links

ENSG00000111875 ∙ NCBI:25842 ∙ OMIM:609189 ∙ HGNC:20995 ∙ Uniprot:Q9Y294 ∙ 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 ASF1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASF1A 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in ASF1A

This is a list of pathogenic ClinVar variants found in the ASF1A region.

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

Position	Type	Phenotype	Significance	ClinVar
6-118894460-C-G		not specified	Uncertain significance (Apr 22, 2022)
6-118894500-G-T		not specified	Uncertain significance (Feb 27, 2023)
6-118905780-T-C			Likely benign (Mar 01, 2023)
6-118905792-A-C		not specified	Uncertain significance (Feb 28, 2023)
6-118907429-C-T		not specified	Uncertain significance (May 26, 2024)
6-118907469-C-T		not specified	Uncertain significance (Sep 27, 2022)
6-118907484-A-G		not specified	Uncertain significance (Nov 08, 2021)
6-118907496-G-A		not specified	Uncertain significance (Jun 30, 2022)
6-118907553-G-A		not specified	Uncertain significance (Apr 08, 2024)
6-118907582-G-A		not specified	Uncertain significance (Mar 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASF1A	protein_coding	protein_coding	ENST00000229595	4	14949

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.805	0.194	124614	0	3	124617	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.39	37	106	0.348	0.00000484	1334
Missense in Polyphen		4	34.449	0.11611		441
Synonymous	-0.292	43	40.6	1.06	0.00000203	390
Loss of Function	2.60	1	9.77	0.102	4.78e-7	118

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone chaperone that facilitates histone deposition and histone exchange and removal during nucleosome assembly and disassembly. Cooperates with chromatin assembly factor 1 (CAF-1) to promote replication-dependent chromatin assembly and with HIRA to promote replication-independent chromatin assembly. Required for the formation of senescence-associated heterochromatin foci (SAHF) and efficient senescence-associated cell cycle exit. {ECO:0000269|PubMed:10759893, ECO:0000269|PubMed:11897662, ECO:0000269|PubMed:12842904, ECO:0000269|PubMed:14718166, ECO:0000269|PubMed:15621527, ECO:0000269|PubMed:15664198, ECO:0000269|PubMed:16151251}.
• Pathway: Formation of Senescence-Associated Heterochromatin Foci (SAHF);DNA Damage/Telomere Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;Cellular responses to external stimuli (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.496
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• pHI: 0.994
• hipred: Y
• hipred_score: 0.716
• ghis: 0.620

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Asf1a
• Phenotype: growth/size/body region phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); embryo phenotype

Gene ontology

• Biological process: osteoblast differentiation;DNA repair;nucleosome assembly;DNA replication-dependent nucleosome assembly;DNA replication-independent nucleosome assembly;negative regulation of chromatin silencing;muscle cell differentiation
• Cellular component: nuclear chromatin;nucleus;nucleoplasm;protein-containing complex
• Molecular function: chromatin binding;protein binding;histone binding