LEKR1

leucine, glutamate and lysine rich 1

Basic information

Region (hg38): 3:156825481-157046129

Links

ENSG00000197980 ∙ NCBI:389170 ∙ OMIM:613536 ∙ HGNC:33765 ∙ Uniprot:Q6ZMV7 ∙ 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 LEKR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LEKR1 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			34	1		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	1	0

Variants in LEKR1

This is a list of pathogenic ClinVar variants found in the LEKR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-156829334-A-G		not specified	Uncertain significance (Mar 22, 2022)
3-156829373-A-G		not specified	Uncertain significance (Dec 27, 2023)
3-156852858-A-G		not specified	Uncertain significance (Jan 04, 2022)
3-156920591-A-T		not specified	Uncertain significance (Apr 06, 2023)
3-156942539-A-G		not specified	Uncertain significance (Nov 08, 2022)
3-156942645-A-T		not specified	Uncertain significance (Jun 11, 2024)
3-156979223-T-A		not specified	Uncertain significance (Nov 17, 2022)
3-156992672-G-A		not specified	Uncertain significance (Jan 02, 2024)
3-156992710-A-T		not specified	Uncertain significance (Jul 25, 2023)
3-156992712-C-T		not specified	Uncertain significance (Oct 29, 2021)
3-156993085-T-C		not specified	Uncertain significance (Jun 16, 2022)
3-156993147-G-A		not specified	Uncertain significance (Aug 04, 2021)
3-156993180-A-C		not specified	Uncertain significance (Aug 09, 2021)
3-156993198-C-T		not specified	Uncertain significance (Dec 28, 2023)
3-157011489-G-A		not specified	Uncertain significance (Aug 23, 2021)
3-157024787-G-A		not specified	Uncertain significance (Nov 28, 2023)
3-157024793-C-T		not specified	Uncertain significance (Feb 16, 2023)
3-157028188-G-A		not specified	Likely benign (Jan 03, 2024)
3-157028221-A-G		not specified	Uncertain significance (Dec 26, 2023)
3-157028233-T-G		not specified	Uncertain significance (Mar 15, 2024)
3-157028262-C-T		not specified	Uncertain significance (Mar 17, 2023)
3-157028269-A-C		not specified	Uncertain significance (Oct 03, 2023)
3-157028301-G-A		not specified	Uncertain significance (Feb 28, 2024)
3-157028302-A-T		not specified	Uncertain significance (Feb 28, 2024)
3-157028332-C-T		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LEKR1	protein_coding	protein_coding	ENST00000491763	4	220649

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.132	0.788	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.685	37	50.7	0.729	0.00000232	891
Missense in Polyphen		6	7.5323	0.79657		94
Synonymous	0.485	14	16.5	0.848	8.63e-7	191
Loss of Function	1.41	2	5.59	0.358	2.35e-7	97

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

Intolerance Scores

• loftool: 0.756
• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.76

Haploinsufficiency Scores

• pHI: 0.144

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.642

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lekr1