LMBRD1 (LMBR1 domain containing 1)

Gene

• Entrez ID: 55788
• Gene name: LMBR1 domain containing 1
• Gene symbol: LMBRD1
• Synonyms: C6orf209, LMBD1, MAHCF, NESI
• Chromosome: 6
• Chromosome location: 6q13
• Summary: This gene encodes a lysosomal membrane protein that may be involved in the transport and metabolism of cobalamin. This protein also interacts with the large form of the hepatitis delta antigen and may be required for the nucleocytoplasmic shuttling of the

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs200639044	C>G	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs749272546	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs779151199	GT>-	Pathogenic	Frameshift variant, coding sequence variant
rs1562112641	G>-	Pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT019020	hsa-miR-335-5p	Microarray	18185580
MIRT1111476	hsa-miR-1305	CLIP-seq
MIRT1111477	hsa-miR-3609	CLIP-seq
MIRT1111478	hsa-miR-3613-3p	CLIP-seq
MIRT1111479	hsa-miR-4307	CLIP-seq
MIRT1111480	hsa-miR-4504	CLIP-seq
MIRT1111481	hsa-miR-4795-3p	CLIP-seq
MIRT1111482	hsa-miR-548ah	CLIP-seq
MIRT1111483	hsa-miR-548t	CLIP-seq
MIRT1111484	hsa-miR-607	CLIP-seq
MIRT2031128	hsa-miR-376c	CLIP-seq
MIRT2031129	hsa-miR-584	CLIP-seq
MIRT2561781	hsa-miR-200b	CLIP-seq
MIRT2561782	hsa-miR-200c	CLIP-seq
MIRT2561783	hsa-miR-3163	CLIP-seq
MIRT2561784	hsa-miR-3651	CLIP-seq
MIRT2561785	hsa-miR-3682-5p	CLIP-seq
MIRT2561786	hsa-miR-369-3p	CLIP-seq
MIRT2561787	hsa-miR-374a	CLIP-seq
MIRT2561788	hsa-miR-374b	CLIP-seq
MIRT2561789	hsa-miR-374c	CLIP-seq
MIRT2561790	hsa-miR-409-3p	CLIP-seq
MIRT2561791	hsa-miR-429	CLIP-seq
MIRT2561792	hsa-miR-4666-3p	CLIP-seq
MIRT2561793	hsa-miR-4766-3p	CLIP-seq
MIRT2561794	hsa-miR-511	CLIP-seq
MIRT2561795	hsa-miR-548c-3p	CLIP-seq
MIRT2561796	hsa-miR-548p	CLIP-seq
MIRT2561797	hsa-miR-570	CLIP-seq
MIRT2561798	hsa-miR-655	CLIP-seq
MIRT2561781	hsa-miR-200b	CLIP-seq
MIRT2561782	hsa-miR-200c	CLIP-seq
MIRT2561783	hsa-miR-3163	CLIP-seq
MIRT2561784	hsa-miR-3651	CLIP-seq
MIRT2561785	hsa-miR-3682-5p	CLIP-seq
MIRT2561786	hsa-miR-369-3p	CLIP-seq
MIRT2561787	hsa-miR-374a	CLIP-seq
MIRT2561788	hsa-miR-374b	CLIP-seq
MIRT2561789	hsa-miR-374c	CLIP-seq
MIRT2561790	hsa-miR-409-3p	CLIP-seq
MIRT2561791	hsa-miR-429	CLIP-seq
MIRT2561792	hsa-miR-4666-3p	CLIP-seq
MIRT2561793	hsa-miR-4766-3p	CLIP-seq
MIRT2561794	hsa-miR-511	CLIP-seq
MIRT2561796	hsa-miR-548p	CLIP-seq
MIRT2561797	hsa-miR-570	CLIP-seq
MIRT2561798	hsa-miR-655	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	25535791
GO:0005765	Component	Lysosomal membrane	IBA	21873635
GO:0005765	Component	Lysosomal membrane	IDA	27456980
GO:0005765	Component	Lysosomal membrane	TAS
GO:0005774	Component	Vacuolar membrane	IBA	21873635
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	27456980
GO:0009235	Process	Cobalamin metabolic process	TAS
GO:0015420	Function	ABC-type vitamin B12 transporter activity	TAS
GO:0015889	Process	Cobalamin transport	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016021	Component	Integral component of membrane	IEA
GO:0016032	Process	Viral process	IEA
GO:0031419	Function	Cobalamin binding	IEA
GO:0043231	Component	Intracellular membrane-bounded organelle	IDA
GO:0061462	Process	Protein localization to lysosome	IBA	21873635
GO:0061462	Process	Protein localization to lysosome	IDA	27456980
GO:0072665	Process	Protein localization to vacuole	IBA	21873635

Other IDs

• MIM: 612625
• HGNC: 23038
• e!Ensembl: ENSG00000168216

Protein

• UniProt ID: Q9NUN5
• Protein name: Lysosomal cobalamin transport escort protein LMBD1 (LMBD1) (HDAg-L-interacting protein NESI) (LMBR1 domain-containing protein 1) (Nuclear export signal-interacting protein)
• Protein function: Lysosomal membrane chaperone required to export cobalamin (vitamin B12) from the lysosome to the cytosol, allowing its conversion to cofactors (PubMed:19136951). Targets ABCD4 transporter from the endoplasmic reticulum to the lysosome (PubMed:27
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF04791	LMBR1	14 → 428	LMBR1-like membrane protein	Family

• Sequence:

  MATSGAASAELVIGWCIFGLLLLAILAFCWIYVRKYQSRRESEVVSTITAIFSLAIALIT
  SALLPVDIFLVSYMKNQNGTFKDWANANVSRQIEDTVLYGYYTLYSVILFCVFFWIPFVY
  FYYEEKDDDDTSKCTQIKTALKYTLGFVVICALLLLVGAFVPLNVPNNKNSTEWEKVKSL
  FEELGSSHGLAALSFSISSLTLIGMLAAITYTAYGMSALPLNLIKGTRSAAYERLENTED
  IEEVEQHIQTIKSKSKDGRPLPARDKRALKQFEERLRTLKKRERHLEFIENSWWTKFCGA
  LRPLKIVWGIFFILVALLFVISLFLSNLDKALHSAGIDSGFIIFGANLSNPLNMLLPLLQ
  TVFPLDYILITIIIMYFIFTSMAGIRNIGIWFFWIRLYKIRRGRTRPQALLFLCMILLLI
  VLHTSYMIYSLAPQYVMYGSQNYLIETNITSDNHKGNSTLSVPKRCDADAPEDQCTVTRT
  YLFLHKFWFFSAAYYFGNWAFLGVFLIGLIVSCCKGKKSVIEGVDEDSDISDDEPSVYSA
  

• Sequence length: 540

Pathways

KEGG:

Vitamin digestion and absorption
Cobalamin transport and metabolism

Reactome:

Cobalamin (Cbl, vitamin B12) transport and metabolism
Defective LMBRD1 causes methylmalonic aciduria and homocystinuria type cblF

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Anemia	Anemia, Megaloblastic	rs118204044, rs118204045, rs118204046, rs121918330, rs869320719, rs869312029, rs121918332, rs869320724, rs767094129, rs786205058, rs786205059, rs137853119, rs137853120, rs137853121, rs1384933966, rs137853122, rs137853123, rs786205060, rs267607121, rs121908584, rs80338697, rs80338699, rs120074166, rs120074167, rs1050828, rs74575103, rs137852314, rs5030868, rs137852316, rs137852317, rs137852318, rs137852319, rs137852320, rs137852321, rs137852322, rs137852323, rs137852324, rs72554665, rs387906468, rs5030872, rs137852326, rs137852333, rs137852327, rs137852328, rs137852329, rs137852330, rs137852331, rs137852332, rs137852334, rs137852335, rs137852336, rs137852339, rs76645461, rs137852340, rs137852341, rs78478128, rs137852343, rs137852344, rs137852345, rs587776730, rs137852346, rs137852347, rs137852349, rs2070404412, rs2070350038, rs2070350009, rs137852303, rs137852304, rs33946267, rs34378160, rs33933298, rs11549407, rs35724775, rs34598529, rs41469945, rs267607201, rs80338694, rs80338696, rs387907018, rs398123546, rs78365220, rs587777100, rs587777101, rs483352840, rs869312752, rs765487627, rs1557229599, rs1557230040, rs1555524842, rs782090947, rs1358275550, rs1557229736, rs1557230573, rs1556323334, rs1233124208, rs1293528130, rs146864395, rs1595503440, rs1603411214, rs137852325, rs1575247302, rs1603411177, rs1336651679, rs782322505
Developmental delay	Global developmental delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291, rs886041382, rs1057518991, rs1057518699, rs753254213, rs748294403, rs762552974, rs1135401795, rs1553121073, rs1553122926, rs1364690005, rs1554086554, rs1554210415, rs1554168326, rs1554776342, rs1553873247, rs1567860112, rs779009256, rs1557447255, rs1564568350, rs780011005, rs1597464953, rs1200336864, rs1569513017, rs1587459606, rs1570332505, rs748888652, rs1575155995, rs2087029320, rs1589669105, rs1601769604, rs1184981709, rs749201074
Developmental regression	Developmental regression	rs1224421127
Homocystinuria	Homocystinuria	rs121964962, rs121964963, rs121964964, rs5742905, rs121964966, rs121964967, rs121964968, rs121964969, rs28934891, rs375846341, rs121964972, rs121964973, rs121434294, rs121434295, rs267606887, rs267606886, rs121434297, rs398123151, rs768434408, rs786204037, rs758206023, rs786204035, rs777661576, rs747846362, rs786204031, rs749765738, rs786204027, rs786204026, rs367585605, rs200137991, rs780014899, rs786204024, rs786204021, rs786204020, rs786204018, rs786204016, rs200100285, rs786204014, rs574132670, rs786204013, rs786204012, rs147257424, rs786204010, rs786204009, rs763539350, rs786204007, rs776483190, rs786204466, rs786204679, rs763036586, rs771298943, rs758236584, rs775351239, rs764160782, rs770095972, rs760214620, rs786204757, rs794727083, rs781444670, rs149119723, rs797044607, rs863223433, rs769080151, rs372010465, rs777919630, rs863223432, rs773734233, rs775992753, rs778220779, rs863223435, rs199948079, rs148865119, rs1057519363, rs759031330, rs1057519362, rs1057519361, rs1057519359, rs779250698, rs886057100, rs1057516895, rs1057516645, rs760417941, rs781567152, rs1057517373, rs746575551, rs766453711, rs1057517435, rs763835246, rs767036273, rs755952006, rs1057517083, rs1057516256, rs751464024, rs1057516552, rs748695461, rs757920190, rs528689432, rs765586205, rs377443637, rs757428597, rs1361324844, rs1347651454, rs1555871188, rs776734688, rs1553187509, rs986604359, rs143124288, rs1553185069, rs866630296, rs1555872787, rs1555873925, rs760609383, rs141502207, rs1555874263, rs1555875325, rs755625628, rs1555876784, rs1555869934, rs1555869958, rs1555869979, rs1434118781, rs1555874121, rs763290176, rs1555874803, rs1555875292, rs1555871095, rs865990681, rs1555876755, rs754980119, rs200688214, rs1568932440, rs1234354755, rs1557761665, rs762065361, rs140277700, rs139645527, rs750323424, rs368321176, rs1170128038, rs1601339216, rs776969786, rs1304669003, rs764338697, rs1380686004, rs1644227125, rs1644375837, rs1981524462, rs373782713, rs1644381879
Methylmalonic acidemia with homocystinuria	METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA, cblF TYPE (disorder), Methylmalonic acidemia with homocystinuria type cblF	rs779151199, rs1562112641, rs118204044, rs118204046, rs397509361, rs118204047, rs397509362, rs118204048, rs397509363, rs397509364, rs398124292, rs387907315, rs2080853826, rs398122908, rs318240758, rs397515485, rs397515487, rs864309743, rs864309742, rs869312686, rs749272546, rs886039425, rs769364566, rs188675529, rs1553454436, rs751828470, rs1379672870, rs1553162317, rs767795583, rs1573878695, rs1385597423, rs1682706954, rs1308639482, rs1380343985, rs1573880177	24664876, 21303734, 19136951, 26997947, 27604308
Neutropenia	Neutropenia	rs879253882
Pancytopenia	Pancytopenia	rs869312883, rs770551610, rs1131690788, rs530073586, rs374333820

Unknown
Disease name	Disease term	dbSNP ID	References
Congenital epicanthus	Congenital Epicanthus
Cystathioninemia	Cystathioninemia
Gamma-cystathionase deficiency	Gamma-cystathionase deficiency
Glossitis	Glossitis
High palate	Byzanthine arch palate
Microtia	Congenital small ears
Psychosis	Psychotic Disorders
Stomatitis	Stomatitis