LMBR1L

protein-coding

limb development membrane protein 1 like

Gene summary

Enables transmembrane signaling receptor activity. Involved in receptor-mediated endocytosis and signal transduction. Located in endoplasmic reticulum membrane and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_018113.4

Inheritance

—

ClinVar variants

P:2U:71B:1

Top phenotype

DSD incomplete virilization

gnomAD constraint

pLI —, LoF o/e 0.75

Max pathogenic AF

—

Genomic locus

chr12:49,097,136-49,110,900

External References & Databases

Ensembl (ENSG00000139636)

Transcript & Mutation Effects

hg38 • Region Span ~13.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LMBR1L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 65

DSD incomplete virilizationTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018113.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense		2 clinvar	67 clinvar	1 clinvar		70
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	2	71	1	0	74

Highest pathogenic variant AF is 0.000049561382

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 72 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018113.4	RefSeq	NP_060583.2	17	MANE Select
ENST00000267102.13	Ensembl	ENSP00000267102.8	17	MANE Select
NM_001300750.2	RefSeq	NP_001287679.1	16	Standard
NM_001300751.2	RefSeq	NP_001287680.1	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

receptor-mediated endocytosis
signal transduction

Molecular Function

transmembrane signaling receptor activity
protein binding

Cellular Component

plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000267102
Coding exons: 17
Length: 13765
Individuals with no LoFs: 125592
Homozygous LoFs: 1
Heterozygous LoFs: 155
Defined: 125748
p: 0.000620

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.781	243	280	0.869	0.0000157	3104
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00049	0.00049	rare
Finnish	0.00056	0.00055	rare
European (Non-Finnish)	0.00091	0.00089	rare
South Asian	0.00052	0.00052	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.108

Gene Damage Prediction

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