LMBR1L

limb development membrane protein 1 like

Basic information

Region (hg38): 12:49097135-49110900

Links

ENSG00000139636 ∙ NCBI:55716 ∙ OMIM:610007 ∙ HGNC:18268 ∙ Uniprot:Q6UX01 ∙ 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 LMBR1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMBR1L 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in LMBR1L

This is a list of pathogenic ClinVar variants found in the LMBR1L region.

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

Position	Type	Phenotype	Significance	ClinVar
12-49097705-G-T		not specified	Uncertain significance (Dec 17, 2023)
12-49097710-C-T		not specified	Uncertain significance (Sep 15, 2021)
12-49097728-G-C		not specified	Uncertain significance (Aug 22, 2023)
12-49097968-G-A		not specified	Uncertain significance (Jun 21, 2023)
12-49098010-G-A		not specified	Uncertain significance (Aug 16, 2021)
12-49100399-G-A		not specified	Uncertain significance (Sep 26, 2023)
12-49100419-G-C		not specified	Uncertain significance (Nov 03, 2023)
12-49100560-G-A		not specified	Uncertain significance (Oct 12, 2021)
12-49100573-C-T		not specified	Uncertain significance (Dec 28, 2022)
12-49100579-A-T		not specified	Uncertain significance (Jun 29, 2023)
12-49100626-A-G		not specified	Uncertain significance (Oct 05, 2021)
12-49101482-C-T		not specified	Uncertain significance (Aug 22, 2023)
12-49101533-A-G		not specified	Uncertain significance (May 30, 2023)
12-49101534-T-C		not specified	Uncertain significance (May 04, 2022)
12-49102125-G-C		not specified	Uncertain significance (Nov 10, 2023)
12-49102187-C-T		DSD incomplete virilization	Likely pathogenic (Sep 01, 2021)
12-49102188-G-A		DSD incomplete virilization	Likely pathogenic (Sep 01, 2021)
12-49102480-G-A		not specified	Uncertain significance (Mar 04, 2024)
12-49102518-T-C		not specified	Uncertain significance (Feb 23, 2023)
12-49102916-C-T		not specified	Uncertain significance (Apr 26, 2023)
12-49103144-T-C		not specified	Uncertain significance (Mar 18, 2024)
12-49103773-A-G		not specified	Uncertain significance (Feb 27, 2024)
12-49104449-T-C		not specified	Uncertain significance (Apr 13, 2022)
12-49104494-A-G		not specified	Uncertain significance (Apr 12, 2024)
12-49104524-G-A		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMBR1L	protein_coding	protein_coding	ENST00000267102	17	13765

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.61e-13	0.382	125592	1	155	125748	0.000620

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.781	243	280	0.869	0.0000157	3104
Missense in Polyphen		95	114.98	0.82622		1371
Synonymous	-0.733	126	116	1.09	0.00000605	1052
Loss of Function	1.27	23	30.6	0.753	0.00000154	330

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000695	0.000693
Ashkenazi Jewish	0.00	0.00
East Asian	0.000493	0.000489
Finnish	0.000559	0.000554
European (Non-Finnish)	0.000912	0.000888
Middle Eastern	0.000493	0.000489
South Asian	0.000523	0.000523
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable LCN1 receptor. May mediate LCN1 endocytosis. {ECO:0000269|PubMed:11287427, ECO:0000269|PubMed:12591932}.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.805
• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.44

Haploinsufficiency Scores

• pHI: 0.313
• hipred: N
• hipred_score: 0.379
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.108

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lmbr1l
• Phenotype: normal phenotype

Gene ontology

• Biological process: receptor-mediated endocytosis;signal transduction
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: transmembrane signaling receptor activity;protein binding