LEMD1

LEM domain containing 1, the group of LEM domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 1:205381378-205455954

Links

ENSG00000186007 ∙ NCBI:93273 ∙ OMIM:610480 ∙ HGNC:18725 ∙ Uniprot:Q68G75 ∙ 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 LEMD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LEMD1 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				1		1
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in LEMD1

This is a list of pathogenic ClinVar variants found in the LEMD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-205381684-C-T		not specified	Uncertain significance (Nov 03, 2023)
1-205381790-G-A		not specified	Likely benign (Nov 07, 2023)
1-205381824-G-A		not specified	Uncertain significance (Dec 27, 2023)
1-205416270-T-C		not specified	Uncertain significance (Dec 02, 2021)
1-205416290-T-G		not specified	Uncertain significance (Dec 03, 2021)
1-205416291-T-C		not specified	Uncertain significance (Apr 01, 2024)
1-205419237-G-T		not specified	Uncertain significance (Dec 27, 2022)
1-205419279-C-T		not specified	Uncertain significance (Nov 30, 2021)
1-205419281-T-C		not specified	Uncertain significance (Jul 09, 2021)
1-205419284-C-G		not specified	Uncertain significance (Nov 29, 2021)
1-205419286-G-T		not specified	Uncertain significance (Apr 08, 2024)
1-205419334-T-C		not specified	Uncertain significance (Nov 14, 2023)
1-205420488-C-T		not specified	Uncertain significance (Jun 19, 2024)
1-205420512-C-T		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LEMD1	protein_coding	protein_coding	ENST00000367153	5	74577

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000334	0.202	125728	0	19	125747	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0363	86	87.0	0.989	0.00000438	1160
Missense in Polyphen		5	5.6066	0.8918		68
Synonymous	-0.459	38	34.6	1.10	0.00000200	341
Loss of Function	-0.210	8	7.38	1.08	4.08e-7	98

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000704	0.0000703
Middle Eastern	0.000217	0.000217
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0964

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.360

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lemd1

Gene ontology

• Cellular component: integral component of membrane