LEFTY1

left-right determination factor 1, the group of Transforming growth factor beta superfamily

Basic information

Region (hg38): 1:225886282-225911382

Previous symbols: [ "LEFTB" ]

Links

ENSG00000243709 ∙ NCBI:10637 ∙ OMIM:603037 ∙ HGNC:6552 ∙ Uniprot:O75610 ∙ 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 LEFTY1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LEFTY1 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				3		3
missense			43	3	4	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	6	4

Variants in LEFTY1

This is a list of pathogenic ClinVar variants found in the LEFTY1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-225886749-A-C		not specified	Uncertain significance (Jun 07, 2024)
1-225886773-C-T		not specified	Uncertain significance (Oct 04, 2022)
1-225886830-C-G		not specified	Uncertain significance (Jan 24, 2023)
1-225886860-G-A		not specified	Uncertain significance (May 04, 2022)
1-225886863-T-G			Benign (Jan 10, 2019)
1-225886878-A-T		not specified	Uncertain significance (May 29, 2024)
1-225886880-G-A			Likely benign (Oct 23, 2018)
1-225886889-A-C			Likely benign (Oct 23, 2018)
1-225886901-C-T			Likely benign (Oct 23, 2018)
1-225886908-T-G		not specified	Uncertain significance (Sep 25, 2024)
1-225886914-G-T		not specified	Uncertain significance (Jun 16, 2023)
1-225886926-G-A		not specified	Uncertain significance (May 17, 2023)
1-225886926-G-T		not specified	Uncertain significance (Mar 19, 2024)
1-225886936-G-A		not specified	Uncertain significance (Aug 21, 2023)
1-225886944-C-T		not specified	Uncertain significance (Aug 27, 2024)
1-225886984-C-T		not specified	Uncertain significance (Apr 22, 2024)
1-225886991-C-A		not specified	Likely benign (Mar 20, 2024)
1-225886993-C-T			Benign (Jun 27, 2018)
1-225887034-C-T		not specified	Uncertain significance (Jul 14, 2024)
1-225887035-G-A		not specified	Uncertain significance (Mar 04, 2024)
1-225887070-G-A		not specified	Uncertain significance (May 16, 2022)
1-225887072-G-T		not specified	Uncertain significance (Sep 13, 2022)
1-225887074-C-T		not specified	Uncertain significance (Mar 07, 2024)
1-225887409-C-A		not specified	Uncertain significance (May 14, 2024)
1-225887412-G-A		not specified	Uncertain significance (May 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LEFTY1	protein_coding	protein_coding	ENST00000272134	4	25101

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.68e-13	0.0113	125675	1	42	125718	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.738	204	236	0.865	0.0000152	2306
Missense in Polyphen		56	62.647	0.89389		641
Synonymous	1.42	97	117	0.832	0.00000828	799
Loss of Function	-0.603	17	14.5	1.17	7.78e-7	134

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000410	0.000409
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000517	0.0000462
European (Non-Finnish)	0.000154	0.000150
Middle Eastern	0.000163	0.000163
South Asian	0.000233	0.000229
Other	0.000509	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for left-right axis determination as a regulator of LEFTY2 and NODAL.
• Pathway: TGF-beta signaling pathway - Homo sapiens (human);Cell Differentiation - Index expanded;Cell Differentiation - Index;Differentiation Pathway;Mesodermal Commitment Pathway;TGF-beta Receptor Signaling;Developmental Biology;Regulation of signaling by NODAL;Signaling by NODAL (Consensus)

Recessive Scores

• pRec: 0.472

Intolerance Scores

• loftool: 0.538
• rvis_EVS: 1.42
• rvis_percentile_EVS: 94.86

Haploinsufficiency Scores

• pHI: 0.520
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.197

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lefty1
• Phenotype: cellular phenotype; growth/size/body region phenotype; respiratory system phenotype; liver/biliary system phenotype; renal/urinary system 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); 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); embryo phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;heart morphogenesis;transforming growth factor beta receptor signaling pathway;determination of left/right symmetry;regulation of signaling receptor activity;positive regulation of pathway-restricted SMAD protein phosphorylation;regulation of apoptotic process;regulation of MAPK cascade;cell development;SMAD protein signal transduction
• Cellular component: extracellular space
• Molecular function: cytokine activity;transforming growth factor beta receptor binding;growth factor activity