LST1

leukocyte specific transcript 1

Basic information

Region (hg38): 6:31586124-31588909

Links

ENSG00000204482 ∙ NCBI:7940 ∙ OMIM:109170 ∙ HGNC:14189 ∙ Uniprot:O00453 ∙ 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 LST1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LST1 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						0
missense			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	1	0

Variants in LST1

This is a list of pathogenic ClinVar variants found in the LST1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31587659-G-A		not specified	Uncertain significance (Jun 07, 2023)
6-31587673-G-A		not specified	Uncertain significance (Apr 13, 2023)
6-31587688-G-C		not specified	Uncertain significance (Dec 19, 2022)
6-31588608-G-T		not specified	Uncertain significance (Jun 10, 2024)
6-31588629-G-A		not specified	Uncertain significance (Oct 12, 2021)
6-31588645-A-C		not specified	Uncertain significance (Nov 07, 2023)
6-31588647-G-A		not specified	Likely benign (Nov 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LST1	protein_coding	protein_coding	ENST00000376093	4	2786

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00113	0.403	125184	0	30	125214	0.000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0137	53	53.3	0.995	0.00000280	642
Missense in Polyphen		27	22.213	1.2155		275
Synonymous	-0.930	30	24.2	1.24	0.00000137	218
Loss of Function	-0.261	4	3.47	1.15	1.48e-7	42

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000122	0.000122
Ashkenazi Jewish	0.00	0.00
East Asian	0.00119	0.00114
Finnish	0.00	0.00
European (Non-Finnish)	0.0000388	0.0000355
Middle Eastern	0.00119	0.00114
South Asian	0.0000357	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible role in modulating immune responses. Induces morphological changes including production of filopodia and microspikes when overexpressed in a variety of cell types and may be involved in dendritic cell maturation. Isoform 1 and isoform 2 have an inhibitory effect on lymphocyte proliferation. {ECO:0000269|PubMed:10706707, ECO:0000269|PubMed:11478849}.

Intolerance Scores

• loftool: 0.284
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.0532
• hipred: N
• hipred_score: 0.123
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lst1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); endocrine/exocrine gland phenotype; immune system phenotype; skeleton 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); reproductive system phenotype

Gene ontology

• Biological process: cell morphogenesis;immune response;regulation of cell shape;anatomical structure morphogenesis;dendrite development;negative regulation of lymphocyte proliferation
• Cellular component: Golgi membrane;cytoplasm;Golgi apparatus;integral component of membrane