CleftGeneDB-Search

Gene: Sec16a

Basic information

Tag	Content
Uniprot ID	E9QAT4; A2AIX1; Q80U43; Q811L5;
Entrez ID	227648
Genbank protein ID	BAC65524.3; AAH42603.1;
Genbank nucleotide ID	XM_006497911.3; NM_153125.2;
Ensembl protein ID	ENSMUSP00000109716; ENSMUSP00000088796;
Ensembl nucleotide ID	ENSMUSG00000026924
Gene name	Protein transport protein Sec16A
Gene symbol	Sec16a
Organism	Mus musculus
NCBI taxa ID	10090
Cleft type
Developmental stage
Data sources	Homology search
Reference
Functional description	Acts as a molecular scaffold that plays a key role in the organization of the endoplasmic reticulum exit sites (ERES), also known as transitional endoplasmic reticulum (tER). SAR1A-GTP-dependent assembly of SEC16A on the ER membrane forms an organized scaffold defining an ERES. Required for secretory cargo traffic from the endoplasmic reticulum to the Golgi apparatus (PubMed:17428803). Mediates the recruitment of MIA3/TANGO to ERES. Regulates both conventional (ER/Golgi-dependent) and GORASP2-mediated unconventional (ER/Golgi-independent) trafficking of CFTR to cell membrane (By similarity). Acts as a RAB10 effector in the regulation of insulin-induced SLC2A4/GLUT4 glucose transporter-enriched vesicles delivery to the plasma membrane in adipocytes (PubMed:27354378).
Sequence	MQPPPQAVPS GVAGPPPAGN PRSMFWANSP YRKPANNAPV APITRPLQPV TDPFAFNRQT 60 LQNTPVGSSS KSSLPNLPGP ALSVFSQWPG LPVTPTNAGD SSTGLHEPLS GTLSQPRADA 120 SLFPPASTPS SLPGLEVSRN AEADPSSGHE VQMLPHSAHY IPGVGPEQPL GGQMNDSGSG 180 PDQPMNRHAP HDGAVTHAAS PFLPQPQMPG QWGPAQGGPQ PSYQHHSPYL EGPVQNMGLQ 240 AASLPHFPPP SSLHQGPGHE SHAPQTFTPA SLASGEGNEI VHQQSKNHPL SSFPPKHTFE 300 QNSRIGNMWA SPELKQNPGV NKEHLLDPAH VNPFTQGNSP ENQAHHPPVA ATNHALQEAA 360 SGALSMFFQG EETENEENLS SEKAGLDKRL NLDSFSSTSR LGHPPPPGAS GVYQAFPRGP 420 SSEAAQEGDA QPYFSQSVGV RLDKQSTVPP ANDAWGDVPG TGTRCASGPQ CENVENLEFV 480 QNQEVLPRET LSVDPFPLSD QIRYGPLPGP AASRPATVGL TRGGGLNLEA PDTPLHPTRP 540 DSVSSSYSSH SHRSPPGSAR PQELVGTFIQ QEVGKLEDDT SGSFFKQIDS SPVGGETDEV 600 TGSQNCCSSL SQPSTPSPPK PTGVFQTSAN SSFEPVKSHL VGVKPVEADR ANMVVEVRGT 660 QYCPKKRRAA VAPPDATSGN LEQPPDNMET PCAPQACPLP LSTTGEAGQL VSNTAGTPLD 720 TVRPVPDKRP SARAQGPVKC ESPATTLWAQ NELPDFGGNV LLAPAAPALY VPVKPKPSEV 780 VHHPEKGMSG QKAWKQGSVP PLQNQDPPGA SENLENPPKV GEEEALPVQA SSGYASLLSS 840 PPTESLHNQP VLIAQPDQSY NLAQPINFSV SLLNPNEKNQ SWGDAVVGER SIVSNNWALG 900 GDPEERAALS GVPASAVTGA SLPSSIPQNC APQGSGSSEM IASQSASWLV QQLSPQTPQS 960 PHPNAEKGPS EFVSSPAGNT SVMLVPPASS TLVPNSNKAK HSSNQEEAVG ALDFTLNRTL 1020 ENPVRMYSPS PSDGPASQQP LPNHPRQSGP GLHNQDHFYQ QVTKDAQDQH RLERAQPELV 1080 PPRPQNSPQV PQASCPEPSN PESPPTQGQS ESLAQPPASP ASVNTGQLLP QPPQASSASV 1140 TSTNSSQAAV RSEQLWLHPP PPNTFGPAPQ DLASYYYYRP LYDAYQSQYP SPYPSDPGTA 1200 SLYYQDMYGL YEPRYRPYDS SASAYAENHR YSEPERPSSR ASHYSDQLAP RQGYPEGYYN 1260 SKSGWSSHSD YYANYYSGQY DYGDPSRWDR YYGSRLRDPR TWDRRYWYDS EHDPYRKDHY 1320 AYSDRPEKCD DHWRYDPRFT GSFDDDAEIH RDPYGEEADR RSIHSEHSAR SLRSTHSLPS 1380 RRSSLSSHSH QSQIYRSHHV TGGSFEAPHA PGSFHGDYAY GTYASNFSGA HGFPEYSYPA 1440 DTSWPAVEQV PSRPTSPEKF TVPHVCARFG PGGQLLKVIP NLPSEGQPAL VEIHSLETLL 1500 QHTPEQEEMR SFPGPLGKDD THKVDVINFA QNKATKCLQN ESLIDKESAS LLWKFIILLC 1560 RQNGTVVGTD IAELLLRDHR TVWLPGKSPN EANLIDFTNE AVEQVEEEES GEAQLSFLTD 1620 SQTVTTSVLE KETERFRELL LYGRKKDALE SAMKNGLWGH ALLLASKMDS RTHARVMTRF 1680 ANSLPINDPL QTVYQLMSGR MPAASTCCGD EKWGDWRPHL AMVLSNLNNN MDVESRTMAT 1740 MGDTLASKGL LDAAHFCYLM AQVGFGVYTK KTTKLVLIGS NHSLPFLKFA TNEAIQRTEA 1800 YEYAQSLGAH TCSLPNFQVF KFIYLCRLAE MGLATQAFHY CEVIAKSVLT QPGAYSPVLI 1860 SQLTQMASQL RLFDPQLKEK PEEESFVEPA WLVQLQHVER QIQEGTVLWS QDGTEPQQCR 1920 ITSGSEVEQS DGPGLNQQAG PQADNPLLMP STEPLMHGVQ LLPTAPQTLP DGQPAHLSRV 1980 PMFPVPMSRG PLELSPAYGP PGSALGFPES SRSDPAVLHP GQALPPTTLS LQESGLPPQE 2040 AKSPDPEMVP RGSPVRHSPP ELSQEEFGES FADPGSSRTA QDLETSPVWD LGSSSLTRAP 2100 SLTSDSEGKK PAQAVKKEPK EPKKTESWFS RWLPGKKRTE AYLPDDKNKS IVWDEKKNQW 2160 VNLNEPEEEK KAPPPPPTSF PRVPQVAPTG PAGPPTASVN VFSRKAGGSR ARYVDVLNPS 2220 GTQRSEPALA PADFFAPLAP LPIPSNLFVP NPDAEEPQPA DGTGCRGQAP AGTQSKAEST 2280 LEPKVGSSTV SAPGPELLPS KPDGSQGGEA PGDHCPTGAP HGGSVPFYNP AQLVQASVTS 2340 GNSRPGRIGQ RKYAALN 2357

Abbreviation :
CLO : cleft lip only. CPO : cleft palate only. CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.

Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

Relation	Gene symbol	Entrez ID	UniProt ID	Species	Evidence	Details
1:1 ortholog	SEC16A	519689	F1N6K7	Bos taurus	Prediction	More>>
1:1 ortholog	SEC16A	102172363	A0A452FDB3	Capra hircus	Prediction	More>>
1:1 ortholog	SEC16A	9919	O15027	Homo sapiens	Publication	More>>
1:1 ortholog	Sec16a	227648	E9QAT4	Mus musculus	Prediction	More>>
1:1 ortholog	SEC16A	464863	A0A2I3RWX9	Pan troglodytes	Prediction	More>>
1:1 ortholog	Sec16a	100360302	D3ZN76	Rattus norvegicus	Prediction	More>>

Identified variants/mutations related to cleft phenotype

Gene symbol	Significant Variants/SNPS	Methods	PubMed ID
SEC16A	c.4484C>T; p.R1495Q	WES and Sanger sequencing	26449438

Other genetic variants/mutations

ID	Variant	Type	Disease	Chromosome\Coordinate	Evidence
rs27201853	p.Pro30Thr	missense variant	-	NC_000068.7:g.26441914G>T	UniProt
rs27201854	p.Met185Thr	missense variant	-	NC_000068.7:g.26441448A>G	UniProt
rs27201856	p.Pro204Ser	missense variant	-	NC_000068.7:g.26441392G>A	UniProt
rs233090362	p.Ser271Phe	missense variant	-	NC_000068.7:g.26441190G>A	UniProt
rs234118048	p.Lys286Glu	missense variant	-	NC_000068.7:g.26441146T>C	UniProt
rs27201857	p.Ala344Glu	missense variant	-	NC_000068.7:g.26440971G>T	UniProt
rs224250361	p.His354Gln	missense variant	-	NC_000068.7:g.26440940A>T	UniProt
rs226653525	p.Leu386Pro	missense variant	-	NC_000068.7:g.26440845A>G	UniProt
rs27201859	p.Asn391Asp	missense variant	-	NC_000068.7:g.26440831T>C	UniProt
rs246996233	p.Ala430Val	missense variant	-	NC_000068.7:g.26440713G>A	UniProt
rs27201860	p.Gln661Glu	missense variant	-	NC_000068.7:g.26440021G>C	UniProt
rs27201861	p.Gln661Arg	missense variant	-	NC_000068.7:g.26440020T>C	UniProt
rs27201863	p.Asn713His	missense variant	-	NC_000068.7:g.26439865T>G	UniProt
rs233137762	p.Pro726Ser	missense variant	-	NC_000068.7:g.26439826G>A	UniProt
rs27201864	p.Asn895Ile	missense variant	-	NC_000068.7:g.26439318T>A	UniProt
rs50804939	p.Met1026Leu	missense variant	-	NC_000068.7:g.26438926T>G	UniProt
rs46054709	p.Met1026Ile	missense variant	-	NC_000068.7:g.26438924C>T	UniProt
rs213593483	p.Ser1094Ala	missense variant	-	NC_000068.7:g.26438722A>C	UniProt
rs27201867	p.Leu1155Pro	missense variant	-	NC_000068.7:g.26438538A>G	UniProt
rs216946670	p.Met1731Val	missense variant	-	NC_000068.7:g.26425812T>C	UniProt
rs583524143	p.Val1898Met	missense variant	-	NC_000068.7:g.26423900C>T	UniProt
rs27201920	p.Pro2008Leu	missense variant	-	NC_000068.7:g.26422124G>A	UniProt
rs216313958	p.Pro2038Leu	missense variant	-	NC_000068.7:g.26422034G>A	UniProt
rs236491298	p.Ser2104Pro	missense variant	-	NC_000068.7:g.26419683A>G	UniProt
rs255929336	p.Gly2264Asp	missense variant	-	NC_000068.7:g.26415368C>T	UniProt
rs227039202	p.Gln2274His	missense variant	-	NC_000068.7:g.26415337C>A	UniProt
rs1134221176	p.Gly2323Val	missense variant	-	NC_000068.7:g.26412873C>A	UniProt
rs242577428	p.Tyr2328Phe	missense variant	-	NC_000068.7:g.26412858T>A	UniProt

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO ID	GO Term	Evidence
GO:0005515	protein binding	IPI

GO:Biological Process

GO ID	GO Term	Evidence
GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	ISO
GO:0007029	endoplasmic reticulum organization	ISS
GO:0007029	endoplasmic reticulum organization	ISO
GO:0007029	endoplasmic reticulum organization	IMP
GO:0007029	endoplasmic reticulum organization	IBA
GO:0007030	Golgi organization	IBA
GO:0032527	protein exit from endoplasmic reticulum	IMP
GO:0034976	response to endoplasmic reticulum stress	ISS
GO:0034976	response to endoplasmic reticulum stress	ISO
GO:0043000	Golgi to plasma membrane CFTR protein transport	ISS
GO:0043000	Golgi to plasma membrane CFTR protein transport	ISO
GO:0048208	COPII vesicle coating	IBA
GO:0050821	protein stabilization	ISS
GO:0050821	protein stabilization	ISO
GO:0070863	positive regulation of protein exit from endoplasmic reticulum	IBA
GO:0070973	protein localization to endoplasmic reticulum exit site	ISS
GO:0070973	protein localization to endoplasmic reticulum exit site	ISO
GO:0070973	protein localization to endoplasmic reticulum exit site	IBA
GO:0072659	protein localization to plasma membrane	IMP

GO:Cellular Component

GO ID	GO Term	Evidence
GO:0000139	Golgi membrane	IEA
GO:0005783	endoplasmic reticulum	ISO
GO:0005789	endoplasmic reticulum membrane	ISO
GO:0005794	Golgi apparatus	ISO
GO:0005829	cytosol	ISS
GO:0005829	cytosol	ISO
GO:0012507	ER to Golgi transport vesicle membrane	IBA
GO:0031090	organelle membrane	ISS
GO:0031090	organelle membrane	ISO
GO:0048471	perinuclear region of cytoplasm	IDA
GO:0070971	endoplasmic reticulum exit site	ISO
GO:0070971	endoplasmic reticulum exit site	IBA
GO:0070971	endoplasmic reticulum exit site	IDA

Reactome Pathway

Reactome ID	Reactome Term	Evidence
R-MMU-199977	ER to Golgi Anterograde Transport	IEA
R-MMU-199991	Membrane Trafficking	IEA
R-MMU-204005	COPII-mediated vesicle transport	IEA
R-MMU-392499	Metabolism of proteins	IEA
R-MMU-446203	Asparagine N-linked glycosylation	IEA
R-MMU-5653656	Vesicle-mediated transport	IEA
R-MMU-597592	Post-translational protein modification	IEA
R-MMU-948021	Transport to the Golgi and subsequent modification	IEA

Functional annotations

Keywords

Keyword ID	Keyword Term
KW-0025	Alternative splicing
KW-0963	Cytoplasm
KW-0256	Endoplasmic reticulum
KW-0931	ER-Golgi transport
KW-0333	Golgi apparatus
KW-0472	Membrane
KW-0492	Microsome
KW-0597	Phosphoprotein
KW-0653	Protein transport
KW-1185	Reference proteome
KW-0813	Transport

Interpro

InterPro ID	InterPro Term
IPR024298	ACE1_Sec16_Sec31
IPR024880	Sec16
IPR024340	Sec16_CCD

PROSITE

PROSITE ID	PROSITE Term

Pfam

Pfam ID	Pfam Term
PF12932	Sec16
PF12931	Sec16_C

Gene: Sec16a

Basic information

Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

Identified variants/mutations related to cleft phenotype

Other genetic variants/mutations

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO:Biological Process

GO:Cellular Component

Reactome Pathway

Functional annotations

Keywords

Interpro

PROSITE

Pfam

Protein-protein interaction

Protein-miRNA interaction