HLTF

helicase like transcription factor, the group of Ring finger proteins

Basic information

Region (hg38): 3:149030127-149086554

Previous symbols: [ "SNF2L3", "SMARCA3" ]

Links

ENSG00000071794 ∙ NCBI:6596 ∙ OMIM:603257 ∙ HGNC:11099 ∙ Uniprot:Q14527 ∙ 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 HLTF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HLTF 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				4	2	6
missense			51	10	5	66
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3		3
non coding					1	1
Total	0	0	51	14	8

Variants in HLTF

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

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

Position	Type	Phenotype	Significance	ClinVar
3-149032267-T-A		not specified	Uncertain significance (Aug 08, 2023)
3-149032348-C-T		not specified	Uncertain significance (Apr 07, 2022)
3-149032367-A-C		not specified	Uncertain significance (Oct 13, 2021)
3-149034988-G-C		not specified	Uncertain significance (Jul 12, 2022)
3-149035005-A-G		HLTF-related disorder	Likely benign (Feb 23, 2021)
3-149039066-C-A		not specified	Uncertain significance (Nov 18, 2022)
3-149039068-C-T		not specified	Uncertain significance (Jun 11, 2021)
3-149039113-G-C		HLTF-related disorder • not specified	Uncertain significance (Jul 07, 2023)
3-149039173-A-G		not specified	Uncertain significance (Oct 10, 2023)
3-149039188-G-T		not specified	Uncertain significance (Sep 07, 2022)
3-149039192-T-C		not specified	Uncertain significance (Apr 11, 2023)
3-149039593-T-A		not specified	Uncertain significance (Mar 28, 2024)
3-149039647-G-A		not specified	Uncertain significance (May 11, 2022)
3-149039685-C-T		HLTF-related disorder	Likely benign (Dec 22, 2020)
3-149040062-T-G		HLTF-related disorder	Likely benign (Sep 01, 2022)
3-149040093-G-A		HLTF-related disorder	Likely benign (Dec 23, 2020)
3-149040122-A-G		HLTF-related disorder	Likely benign (Nov 12, 2020)
3-149040123-T-C		not specified	Uncertain significance (Nov 07, 2022)
3-149041495-C-T		not specified	Uncertain significance (Jul 05, 2023)
3-149041582-T-C			Benign (Jul 06, 2018)
3-149042174-C-T		HLTF-related disorder	Likely benign (Mar 11, 2024)
3-149042177-T-C		HLTF-related disorder • not specified	Likely benign (Mar 16, 2022)
3-149042258-T-A		not specified	Uncertain significance (Sep 28, 2022)
3-149042263-T-C		HLTF-related disorder	Likely benign (Aug 21, 2024)
3-149046093-C-T		HLTF-related disorder	Uncertain significance (Oct 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HLTF	protein_coding	protein_coding	ENST00000310053	25	56428

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.87e-28	0.00219	125405	2	340	125747	0.00136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	441	506	0.872	0.0000251	6613
Missense in Polyphen		157	196.46	0.79914		2626
Synonymous	1.82	140	170	0.822	0.00000841	1829
Loss of Function	0.937	47	54.5	0.863	0.00000272	737

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00230	0.00230
Ashkenazi Jewish	0.00	0.00
East Asian	0.000612	0.000598
Finnish	0.00689	0.00681
European (Non-Finnish)	0.000730	0.000721
Middle Eastern	0.000612	0.000598
South Asian	0.00111	0.00105
Other	0.00219	0.00212

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has both helicase and E3 ubiquitin ligase activities. Possesses intrinsic ATP-dependent nucleosome-remodeling activity; This activity may be required for transcriptional activation or repression of specific target promoters (By similarity). These may include the SERPINE1 and HIV-1 promoters and the SV40 enhancer, to which this protein can bind directly. Plays a role in error-free postreplication repair (PRR) of damaged DNA and maintains genomic stability through acting as a ubiquitin ligase for 'Lys-63'-linked polyubiquitination of chromatin-bound PCNA. {ECO:0000250, ECO:0000269|PubMed:10391891, ECO:0000269|PubMed:18316726, ECO:0000269|PubMed:18719106, ECO:0000269|PubMed:7876228, ECO:0000269|PubMed:8672239, ECO:0000269|PubMed:9126292}.
• Pathway: Retinoblastoma (RB) in Cancer;Post-translational protein modification;Metabolism of proteins;Protein ubiquitination;E3 ubiquitin ligases ubiquitinate target proteins (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.0816
• rvis_EVS: 0.96
• rvis_percentile_EVS: 90.19

Haploinsufficiency Scores

• pHI: 0.498
• hipred: Y
• hipred_score: 0.575
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.912

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hltf
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm; 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); 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); cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: chromatin organization;regulation of transcription, DNA-templated;protein ubiquitination;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;membrane
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;RNA binding;helicase activity;protein binding;ATP binding;zinc ion binding;ATPase activity;ubiquitin protein ligase binding;ubiquitin protein ligase activity