HBS1L

HBS1 like translational GTPase, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 6:134960377-135103056

Links

ENSG00000112339 ∙ NCBI:10767 ∙ OMIM:612450 ∙ HGNC:4834 ∙ Uniprot:Q9Y450 ∙ 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 HBS1L gene.

• Inborn genetic diseases (12 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HBS1L 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			12		2	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	12	2	2

Variants in HBS1L

This is a list of pathogenic ClinVar variants found in the HBS1L region.

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

Position	Type	Phenotype	Significance	ClinVar
6-134966324-A-C			Benign (Dec 31, 2019)
6-134966451-C-T		not specified	Uncertain significance (Oct 14, 2023)
6-134978710-T-C		not specified	Uncertain significance (Oct 17, 2023)
6-134978767-C-T		not specified	Uncertain significance (Jan 03, 2024)
6-134978779-C-T		not specified	Uncertain significance (May 24, 2023)
6-134979218-C-T		not specified	Uncertain significance (Dec 01, 2022)
6-134979224-C-T		not specified	Uncertain significance (Oct 05, 2021)
6-134982499-C-T		not specified	Uncertain significance (Aug 16, 2022)
6-134985353-C-G		not specified	Uncertain significance (Nov 08, 2022)
6-134986771-T-C		not specified	Uncertain significance (Mar 04, 2024)
6-134987715-C-T		not specified	Uncertain significance (Nov 12, 2021)
6-134987790-G-A		not specified	Uncertain significance (Aug 30, 2022)
6-134993774-A-T		not specified	Uncertain significance (Dec 15, 2023)
6-134997435-C-T		not specified	Uncertain significance (Apr 05, 2023)
6-134997600-A-G		not specified	Uncertain significance (Feb 06, 2023)
6-135002789-C-T		not specified	Uncertain significance (Nov 08, 2022)
6-135002821-G-A		not specified	Uncertain significance (Nov 03, 2023)
6-135002823-C-G			Benign (May 16, 2018)
6-135002834-C-T			Benign (Jun 28, 2018)
6-135002837-G-C		not specified	Uncertain significance (Oct 14, 2023)
6-135039662-T-G		not specified	Uncertain significance (Apr 18, 2023)
6-135042039-T-C		not specified	Uncertain significance (Jan 19, 2024)
6-135042063-T-G		not specified	Uncertain significance (Dec 06, 2021)
6-135042088-C-T		not specified	Uncertain significance (Nov 17, 2022)
6-135050592-C-T			Likely benign (Mar 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HBS1L	protein_coding	protein_coding	ENST00000367837	18	142679

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.86e-7	1.00	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.890	316	364	0.869	0.0000190	4459
Missense in Polyphen		129	166.78	0.77346		2088
Synonymous	0.629	123	132	0.930	0.00000754	1313
Loss of Function	3.17	18	39.5	0.456	0.00000222	466

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000400	0.000394
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000267	0.000264
Middle Eastern	0.000165	0.000163
South Asian	0.000101	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Legionellosis - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);Metabolism of RNA;mRNA decay by 3, to 5, exoribonuclease;Deadenylation-dependent mRNA decay (Consensus)

Recessive Scores

• pRec: 0.252

Intolerance Scores

• loftool: 0.450
• rvis_EVS: 1.23
• rvis_percentile_EVS: 93.25

Haploinsufficiency Scores

• pHI: 0.419
• hipred: N
• hipred_score: 0.426
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.859

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hbs1l
• Phenotype: homeostasis/metabolism phenotype; craniofacial 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); immune system phenotype; skeleton phenotype; vision/eye phenotype; hematopoietic system phenotype; reproductive system phenotype; pigmentation phenotype

Gene ontology

• Biological process: translation;translational elongation;signal transduction;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
• Cellular component: cytosol;membrane;extracellular exosome
• Molecular function: translation elongation factor activity;GTPase activity;GTP binding