RSF1

remodeling and spacing factor 1, the group of PHD finger proteins

Basic information

Region (hg38): 11:77660009-77820869

Previous symbols: [ "HBXAP" ]

Links

ENSG00000048649 ∙ NCBI:51773 ∙ OMIM:608522 ∙ HGNC:18118 ∙ Uniprot:Q96T23 ∙ 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 RSF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RSF1 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		2
missense			50	4		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	6	0

Variants in RSF1

This is a list of pathogenic ClinVar variants found in the RSF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-77667000-C-T		not specified	Uncertain significance (Mar 21, 2022)
11-77667022-A-C		not specified	Uncertain significance (Jun 02, 2024)
11-77667053-T-C		not specified	Uncertain significance (May 09, 2023)
11-77667119-C-T		not specified	Uncertain significance (May 26, 2022)
11-77667174-C-T		not specified	Uncertain significance (Mar 18, 2024)
11-77667230-T-C		not specified	Uncertain significance (Nov 03, 2023)
11-77667339-G-A		not specified	Uncertain significance (Jan 23, 2024)
11-77667353-C-T		not specified	Uncertain significance (Dec 27, 2023)
11-77667369-C-T		not specified	Uncertain significance (Mar 29, 2022)
11-77667390-C-T		not specified	Uncertain significance (Aug 13, 2021)
11-77667401-T-C		not specified	Uncertain significance (Dec 19, 2023)
11-77667403-C-T			Likely benign (Mar 01, 2022)
11-77667411-T-C		not specified	Uncertain significance (Apr 08, 2024)
11-77667437-C-T		not specified	Likely benign (Jan 27, 2022)
11-77667438-G-A		not specified	Uncertain significance (Dec 19, 2022)
11-77672092-T-G		not specified	Uncertain significance (Mar 21, 2022)
11-77672121-G-A			Likely benign (Apr 01, 2023)
11-77672203-T-C		not specified	Uncertain significance (Dec 15, 2022)
11-77675069-C-T		not specified	Uncertain significance (Feb 28, 2024)
11-77675185-T-C		not specified	Uncertain significance (Mar 26, 2024)
11-77675249-C-T		not specified	Uncertain significance (Mar 01, 2023)
11-77676832-C-A		not specified	Uncertain significance (Jan 23, 2024)
11-77676892-C-T		not specified	Uncertain significance (May 20, 2024)
11-77676945-A-G		not specified	Uncertain significance (Mar 02, 2023)
11-77676990-C-G		not specified	Uncertain significance (May 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RSF1	protein_coding	protein_coding	ENST00000308488	16	161023

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.72e-11	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.77	620	757	0.819	0.0000399	9552
Missense in Polyphen		206	310.49	0.66348		3722
Synonymous	0.298	259	265	0.977	0.0000134	2603
Loss of Function	7.63	0	67.8	0.00	0.00000427	846

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for assembly of regular nucleosome arrays by the RSF chromatin-remodeling complex (PubMed:12972596). Facilitates transcription of hepatitis B virus (HBV) genes by the pX transcription activator. In case of infection by HBV, together with pX, it represses TNF-alpha induced NF-kappa-B transcription activation. Represses transcription when artificially recruited to chromatin by fusion to a heterogeneous DNA binding domain (PubMed:11944984, PubMed:11788598). {ECO:0000269|PubMed:11788598, ECO:0000269|PubMed:11944984, ECO:0000269|PubMed:12972596}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: 0.39
• rvis_percentile_EVS: 75.7

Haploinsufficiency Scores

• pHI: 0.826
• hipred: Y
• hipred_score: 0.704
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.570

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rsf1
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); vision/eye 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); embryo phenotype; skeleton phenotype; limbs/digits/tail phenotype

Gene ontology

• Biological process: nucleosome assembly;chromatin remodeling;DNA-templated transcription, initiation;histone acetylation;nucleosome positioning;CENP-A containing nucleosome assembly;negative regulation of DNA binding;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of viral transcription
• Cellular component: histone acetyltransferase complex;nuclear chromatin;nucleus;nucleoplasm;RSF complex
• Molecular function: histone acetyltransferase activity;protein binding;ATPase activity;histone binding;metal ion binding