NBAS (NBAS subunit of NRZ tethering complex)

Gene

• Entrez ID: 51594
• Gene name: NBAS subunit of NRZ tethering complex
• Gene symbol: NBAS
• Synonyms (NCBI Gene): ILFS2, NAG, SOPH
• Chromosome: 2
• Chromosome location: 2p24.3
• Summary: This gene encodes a protein with two leucine zipper domains, a ribosomal protein S14 signature domain and a Sec39 like domain. The protein is thought to be involved in Golgi-to-ER transport. Mutations in this gene are associated with short stature, optic

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs75566418	A>G	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, non coding transcript variant, missense variant
rs140256463	G>A	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant, genic upstream transcript variant
rs143212851	A>C	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant, genic upstream transcript variant
rs143724414	T>C	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, missense variant
rs199717686	T>G	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs201084909	T>A	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs368085185	G>A	Pathogenic	Non coding transcript variant, intron variant, missense variant, coding sequence variant, genic upstream transcript variant
rs368196005	A>C	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs369698072	C>A,T	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs370526257	G>A	Likely-pathogenic	Genic upstream transcript variant, non coding transcript variant, coding sequence variant, missense variant
rs748880753	T>C,G	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, non coding transcript variant, missense variant
rs759315662	->A	Pathogenic	Genic upstream transcript variant, frameshift variant, coding sequence variant, non coding transcript variant
rs759960319	G>A,C	Pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant, non coding transcript variant, stop gained
rs761330483	G>A,T	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant, genic upstream transcript variant, stop gained
rs764164808	A>C	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant, genic upstream transcript variant
rs770446752	C>A,T	Pathogenic	Missense variant, stop gained, coding sequence variant, genic upstream transcript variant, non coding transcript variant
rs776597537	C>G,T	Pathogenic	Synonymous variant, non coding transcript variant, coding sequence variant, intron variant
rs776797592	T>-,TT	Likely-pathogenic, pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs796052121	A>G	Likely-pathogenic, pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs796065037	TCA>-	Pathogenic	Genic upstream transcript variant, coding sequence variant, intron variant, non coding transcript variant, inframe deletion
rs796065038	GAG>-	Pathogenic	Genic upstream transcript variant, coding sequence variant, intron variant, non coding transcript variant, inframe deletion
rs1064795199	G>-	Likely-pathogenic	Non coding transcript variant, frameshift variant, genic upstream transcript variant, 5 prime UTR variant, coding sequence variant
rs1064795471	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant, intron variant
rs1085307944	C>A	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs1131692171	G>A	Pathogenic	Non coding transcript variant, intron variant, genic upstream transcript variant, coding sequence variant, stop gained
rs1278049478	G>A,C	Pathogenic	Genic upstream transcript variant, non coding transcript variant, coding sequence variant, missense variant, stop gained
rs1553308501	A>C	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1553348090	T>C	Likely-pathogenic	Splice acceptor variant
rs1553367857	G>T	Likely-pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1572903776	C>-	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant, genic upstream transcript variant
rs1573008071	C>T	Likely-pathogenic	Splice donor variant, genic upstream transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT440142	hsa-miR-432-5p	HITS-CLIP	24374217
MIRT440142	hsa-miR-432-5p	HITS-CLIP	24374217
MIRT1174722	hsa-miR-4434	CLIP-seq
MIRT1174723	hsa-miR-4516	CLIP-seq
MIRT1174724	hsa-miR-4531	CLIP-seq
MIRT1174725	hsa-miR-4643	CLIP-seq
MIRT1174726	hsa-miR-466	CLIP-seq
MIRT1174727	hsa-miR-4789-3p	CLIP-seq
MIRT2050546	hsa-miR-4328	CLIP-seq
MIRT2050547	hsa-miR-582-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000149	Function	SNARE binding	IBA
GO:0000149	Function	SNARE binding	IDA	19369418
GO:0000956	Process	Nuclear-transcribed mRNA catabolic process	IMP	23828042
GO:0005515	Function	Protein binding	IPI	29929043
GO:0005737	Component	Cytoplasm	IEA
GO:0005783	Component	Endoplasmic reticulum	IDA	19369418
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006890	Process	Retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	IBA
GO:0006890	Process	Retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	IEA
GO:0006890	Process	Retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	IMP	19369418
GO:0006890	Process	Retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	NAS	15029241
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IEA
GO:0070939	Component	Dsl1/NZR complex	IBA
GO:0070939	Component	Dsl1/NZR complex	IDA	20462495
GO:0070939	Component	Dsl1/NZR complex	IPI	20462495
GO:2000623	Process	Negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IMP	23828042

Other IDs

• MIM: 608025
• HGNC: 15625
• e!Ensembl: ENSG00000151779

Protein

• UniProt ID: A2RRP1
• Protein name: NBAS subunit of NRZ tethering complex (Neuroblastoma-amplified gene protein) (Neuroblastoma-amplified sequence)
• Protein function: Involved in Golgi-to-endoplasmic reticulum (ER) retrograde transport; the function is proposed to depend on its association in the NRZ complex which is believed to play a role in SNARE assembly at the ER (PubMed:19369418). Required for normal em
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF15492	Nbas_N	90 → 371	Neuroblastoma-amplified sequence, N terminal	Family
  PF08314	Sec39	726 → 1054	Secretory pathway protein Sec39	Family
  PF08314	Sec39	1014 → 1376	Secretory pathway protein Sec39	Family

• Tissue specificity: TISSUE SPECIFICITY: Broadly expressed, with highest levels in heart and skeletal muscle, and lowest levels in liver, small intestine and thymus. Well expressed in retinal ganglion cells, epidermal skin cells, and leukocytes. Up-regulated together with N-m
• Sequence:

  MAAPESGPALSPGTAEGEEETILYDLLVNTEWPPETEVQPRGNQKHGASFIITKAIRDRL
  LFLRQYIWYSPAPFLLPDGLVRLVNKQINWHLVLASNGKLLAAVQDQCVEIRSAKDDFTS
  IIGKCQVPKDPKPQWRRVAWSYDCTLLAYAESTGTVRVFDLMGSELFVISPASSFIGDLS
  YAIAGLIFLEYKASAQWSAELLVINYRGELRSYLVSVGTNQSYQESHCFSFSSHYPHGIN
  TAIYHPGHRLLLVGGCETAEVGMSKASSCGLSAWRVLSGSPYYKQVTNGGDGVTAVPKTL
  GLLRMLSVKFYSRQGQEQDGIFKMSLSPDGMLLAAIHFSGKLSIWAIPSLKQQGEWGQNE
  QPGYDDLNPDWRLSTEKRKKIKDKESFYPLIDVNWWADSAVTLARCSGALTVSSVKTLKN
  LLGKSCEWFEPSPQVTATHDGGFLSLECEIKLAPKRSRLETRAGEEDEGEEDSDSDYEIS
  AKARYFGYIKQGLYLVTEMERFAPPRKRPRTITKNYRLVSLRSTTPEELYQRKIESEEYE
  EALSLAHTYGLDTDLVYQRQWRKSAVNVASIQNYLSKIKKRSWVLHECLERVPENVDAAK
  ELLQYGLKGTDLEALLAIGKGADDGRFTLPGEIDIDSISYEELSPPDEEPAKNKKEKELK
  KRQELLKLVNFSKLTLEQKELCRCRRKLLTYLDRLATYEEILGVPHASEQRYDAEFFKKF
  RNQNIVLSARTYAQESNVQALEILFTYHGSDLLPHRLAILSNFPETTSPHEYSVLLPEAC
  FNGDSLMIIPWHEHKHRAKDWCEELACRMVVEPNLQDESEFLYAAQPELLRFRMTQLTVE
  KVMDWYQTRAEEIEHYARQVDCALSLIRLGMERNIPGLLVLCDNLVTLETLVYEARCDVT
  LTLKELQQMKDIEKLRLLMNSCSEDKYVTSAYQWMVPFLHRCEKQSPGVANELLKEYLVT
  LAKGDLKFPLKIFQHSKPDLQQKIIPDQDQLMAIALECIYTCERNDQLCLCYDLLECLPE
  RGYGDKTEATTKLHDMVDQLEQILSVSELLEKHGLEKPISFVKNTQSSSEEARKLMVRLT
  RHTGRKQPPVSESHWRTLLQDMLTMQQNVYTCLDSDACYEIFTESLLCSSRLENIHLAGQ
  MMHCSACSENPPAGIAHKGKPHYRVSYEKSIDLVLAASREYFNSSTNLTDSCMDLARCCL
  QLITDRPPAIQEELDLIQAVGCLEEFGVKILPLQVRLCPDRISLIKECISQSPTCYKQST
  KLLGLAELLRVAGENPEERRGQVLILLVEQALRFHDYKAASMHCQELMATGYPKSWDVCS
  QLGQSEGYQDLATRQELMAFALTHCPPSSIELLLAASSSLQTEILYQRVNFQIHHEGGEN
  ISASPLTSKAVQEDEVGVPGSNSADLLRWTTATTMKVLSNTTTTTKAVLQAVSDGQWWKK
  SLTYLRPLQGQKCGGAYQIGTTANEDLEKQGCHPFYESVISNPFVAESEGTYDTYQHVPV
  ESFAEVLLRTGKLAEAKNKGEVFPTTEVLLQLASEALPNDMTLALAYLLALPQVLDANRC
  FEKQSPSALSLQLAAYYYSLQIYARLAPCFRDKCHPLYRADPKELIKMVTRHVTRHEHEA
  WPEDLISLTKQLHCYNERLLDFTQAQILQGLRKGVDVQRFTADDQYKRETILGLAETLEE
  SVYSIAISLAQRYSVSRWEVFMTHLEFLFTDSGLSTLEIENRAQDLHLFETLKTDPEAFH
  QHMVKYIYPTIGGFDHERLQYYFTLLENCGCADLGNCAIKPETHIRLLKKFKVVASGLNY
  KKLTDENMSPLEALEPVLSSQNILSISKLVPKIPEKDGQMLSPSSLYTIWLQKLFWTGDP
  HLIKQVPGSSPEWLHAYDVCMKYFDRLHPGDLITVVDAVTFSPKAVTKLSVEARKEMTRK
  AIKTVKHFIEKPRKRNSEDEAQEAKDSKVTYADTLNHLEKSLAHLETLSHSFILSLKNSE
  QETLQKYSHLYDLSRSEKEKLHDEAVAICLDGQPLAMIQQLLEVAVGPLDISPKDIVQSA
  IMKIISALSGGSADLGGPRDPLKVLEGVVAAVHASVDKGEELVSPEDLLEWLRPFCADDA
  WPVRPRIHVLQILGQSFHLTEEDSKLLVFFRTEAILKASWPQRQVDIADIENEENRYCLF
  MELLESSHHEAEFQHLVLLLQAWPPMKSEYVITNNPWVRLATVMLTRCTMENKEGLGNEV
  LKMCRSLYNTKQMLPAEGVKELCLLLLNQSLLLPSLKLLLESRDEHLHEMALEQITAVTT
  VNDSNCDQELLSLLLDAKLLVKCVSTPFYPRIVDHLLASLQQGRWDAEELGRHLREAGHE
  AEAGSLLLAVRGTHQAFRTFSTALRAAQHWV

• Sequence length: 2371

Pathways

Reactome:

COPI-dependent Golgi-to-ER retrograde traffic

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Acute infantile liver failure due to synthesis defect of mtDNA-encoded proteins	Pathogenic; Likely pathogenic	rs143012720, rs376113678, rs2148225587, rs1680038424, rs368516200, rs2148636532, rs1676898074, rs2528283195, rs1355806716, rs199627281, rs1232631800, rs759315662, rs1558509149, rs368085185, rs1042786545, rs1478754689, rs556229592, rs867909116, rs776797592, rs776597537	RCV006266740 RCV002222731 RCV003479364 RCV005419261 RCV002266488 RCV005433190 RCV002302548 RCV002302549 RCV002470102 RCV003404037 RCV003485816 RCV002469052 RCV003226556 RCV003401097 RCV003123497 RCV003485862 RCV003479963 RCV005063190 RCV003479169 RCV005897284
Infantile liver failure	Likely pathogenic; Pathogenic	rs776797592, rs761330483	RCV000602655 RCV000607971
Infantile liver failure syndrome 2	Pathogenic; Likely pathogenic	rs1669613513, rs143012720, rs2148233321, rs2148464034, rs2148574197, rs2148636494, rs1663675984, rs376113678, rs1253033456, rs1176007591, rs1572813576, rs368516200, rs1268309894, rs767908363, rs1339816196, rs138546465, rs372603397, rs758863985, rs1673479296, rs780108348, rs765420811, rs1253502123, rs1442013338, rs796065037, rs759315662, rs368196005, rs796052121, rs368085185, rs768154511, rs1671171740, rs767084659, rs763573768, rs908833503, rs1064795471, rs770446752, rs776797592, rs759960319, rs776597537, rs1573008071, rs202020492, rs1019313682, rs200365734, rs767280377	RCV001334881 RCV005023152 RCV001647343 RCV001647342 RCV004040801 RCV001795817 RCV004785322 RCV002267780 RCV002267781 RCV005023498 RCV002471199 RCV005025473 RCV005014746 RCV005016954 RCV005025499 RCV005017002 RCV005023470 RCV005025527 RCV002251027 RCV005017170 RCV005025788 RCV005019318 RCV005025933 RCV000186577 RCV000186578 RCV000186579 RCV000186581 RCV000202648 RCV003148127 RCV005022009 RCV005015037 RCV003990085 RCV004566598 RCV005018810 RCV000492542 RCV002491216 RCV000755658 RCV000755659 RCV000986591 RCV005021354 RCV001089504 RCV001251622 RCV001254351
Monogenic short statue	Likely pathogenic; Pathogenic	rs776797592	RCV005865358
NBAS-related disorder	Likely pathogenic; Pathogenic	rs138546465, rs759315662, rs1478754689, rs1558275372, rs2528030864, rs770446752	RCV003893046 RCV003947561 RCV004750872 RCV003400335 RCV003412318 RCV003900026
Retinal dystrophy	Pathogenic	rs376113678	RCV004815643
See cases	Pathogenic; Likely pathogenic	rs1478754689, rs2527905126	RCV003156176 RCV003156177
	Pathogenic; Likely pathogenic	rs143012720, rs1663675984, rs1176007591, rs368516200, rs1268309894, rs767908363, rs1339816196, rs138546465, rs372603397, rs758863985, rs1573008071, rs780108348, rs2148636532, rs2148090502, rs765420811, rs1253502123, rs1442013338, rs759315662, rs796052121, rs768154511, rs1671171740, rs767084659, rs908833503, rs1064795471, rs1131692171, rs369698072, rs776797592, rs776597537, rs202020492, rs200365734, rs767280377	RCV005023152 RCV001809206 RCV005023498 RCV005025473 RCV005014746 RCV005016954 RCV005025499 RCV005017002 RCV005023470 RCV005025527 RCV004785459 RCV002260558 RCV002273846 RCV002273847 RCV005025788 RCV005019318 RCV005025933 RCV005016530 RCV000761305 RCV003148126 RCV005022009 RCV005015037 RCV004566597 RCV005018810 RCV000495259 RCV000030702 RCV002491216 RCV002260517 RCV005021354 RCV001251622 RCV001254351
Thyroid cancer, nonmedullary, 1	Likely pathogenic; Pathogenic	rs776597537	RCV005897285

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Acute myeloid leukemia	Benign	rs16862767, rs56336903	RCV005915521 RCV005917377
Cervical cancer	Benign	rs35454315	RCV005913004
Cholangiocarcinoma	Benign	rs6717303	RCV005919654
Clear cell carcinoma of kidney	Likely benign	rs144760143	RCV005907616
Familial cancer of breast	Uncertain significance	rs375991089	RCV005922846
Gastric cancer	Benign; Uncertain significance	rs35454315, rs16862767, rs375854696	RCV005913005 RCV005915523 RCV005924336
Growth failure in early childhood	Uncertain significance; Conflicting classifications of pathogenicity	rs371186583, rs764292893	RCV006437215 RCV006437216
Hepatocellular carcinoma	Benign	rs35454315	RCV005913002
Lung cancer	Benign	rs10202600	RCV005915718
Malignant lymphoma, large B-cell, diffuse	Benign	rs11900088	RCV005925136
Malignant tumor of esophagus	Benign	rs35454315, rs35295359	RCV005913003 RCV005904381
Neurodevelopmental disorder	Uncertain significance; Conflicting classifications of pathogenicity	rs200532922, rs796065038	RCV003389075 RCV003389048
Optic atrophy	Uncertain significance; Conflicting classifications of pathogenicity	rs1036475904, rs144520644, rs749416685, rs573592083, rs776271105	RCV004816842 RCV004816878 RCV004815716 RCV004818229 RCV004817176
Ovarian serous cystadenocarcinoma	Benign	rs16862767, rs56336903, rs35295359	RCV005915524 RCV005917378 RCV005904382
Pituitary stalk interruption syndrome	Uncertain significance	rs1680274433	RCV001257297
Sarcoma	Benign	rs16862767	RCV005915522
Schizophrenia	Uncertain significance	rs2528757943	RCV002463531
Thymoma	Benign	rs56336903	RCV005917380
Uterine carcinosarcoma	Benign; Conflicting classifications of pathogenicity	rs6717303, rs10202600, rs56336903, rs140868609	RCV005919653 RCV005915717 RCV005917379 RCV005893651
Uterine corpus endometrial carcinoma	Benign	rs56336903	RCV005917381

Associations from Text Mining
Disease Name	Relationship Type	References
adult multisystem inflammatory disease COVID 19 related	Associate	34288298
Blood Coagulation Disorders	Associate	28629372
Body Dysmorphic Disorders	Associate	36479642
Carcinogenesis	Associate	40028213
Carcinoma Renal Cell	Associate	39838718
Chemical and Drug Induced Liver Injury	Associate	27789416, 28611345
Cone Dystrophy	Associate	36479642
COVID 19	Associate	36768954
Death	Associate	23621803
Developmental Disabilities	Associate	27789416
Diabetes Mellitus Type 2	Associate	28611345
Facial Dysmorphism with Multiple Malformations	Associate	34288298
Fever	Associate	26073778, 28611345, 28629372, 34427841
GATA2 Deficiency	Associate	34386911
Growth Disorders	Associate	20577004, 27789416, 34288298, 34386911, 36479642, 40215727
HEM dysplasia	Associate	34288298
Hyperammonemia	Associate	34427841
Immune System Diseases	Associate	34288298
Immunologic Deficiency Syndromes	Associate	27789416, 34386911, 35902954
Immunologic Deficiency Syndromes	Inhibit	40215727
Infections	Associate	34386911
Jaundice	Associate	28629372
Liver Diseases	Associate	28611345
Liver Failure	Associate	28611345, 28629372
Liver Failure Acute	Associate	26073778, 28629372, 28946922, 30845840, 33542026, 34288298, 34386911, 34427841, 35349761, 36479642
Lymphohistiocytosis Hemophagocytic	Associate	35902954
Microcephaly	Associate	34427841
Microphthalmia Syndromic 10	Associate	34427841
Multiple System Atrophy	Associate	34386911
Muscle Hypotonia	Associate	34427841
Neoplastic Syndromes Hereditary	Associate	20577004
Neuroblastoma	Associate	11464910, 23621803, 23991058, 27789416, 34427841, 36479642
Neuroectodermal Tumors Primitive Peripheral	Stimulate	10882752
Optic Atrophy	Associate	20577004, 27789416, 33270637, 36479642, 40215727
Osteogenesis Imperfecta	Associate	27789416, 33542026
Osteoporosis pseudoglioma syndrome	Associate	27789416
Pelger Huet Anomaly	Associate	20577004, 27789416, 34288298, 36479642, 40215727
Syndrome	Associate	27789416, 36479642