NHEJ1 (non-homologous end joining factor 1)

Gene

• Entrez ID: 79840
• Gene name: Non-homologous end joining factor 1
• Gene symbol: NHEJ1
• Synonyms: IMD124, MCOPCB13, XLF
• Chromosome: 2
• Chromosome location: 2q35
• Summary: Double-strand breaks in DNA result from genotoxic stresses and are among the most damaging of DNA lesions. This gene encodes a DNA repair factor essential for the nonhomologous end-joining pathway, which preferentially mediates repair of double-stranded b

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs118204451	G>A,C	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant, missense variant
rs118204452	A>G	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs118204453	G>A,T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant, synonymous variant
rs786205547	C>G	Likely-pathogenic	Splice donor variant
rs886037606	TAC>AA	Pathogenic	Splice donor variant, intron variant
rs886037607	->A	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs886041973	->C	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1064793763	T>A	Pathogenic	Splice acceptor variant
rs1064796857	AATC>-	Likely-pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1064797028	A>C	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs1064797042	A>-	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1553542017	G>A	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1553548393	->TTCC	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1184236	hsa-miR-193a-5p	CLIP-seq
MIRT1184237	hsa-miR-3064-5p	CLIP-seq
MIRT1184238	hsa-miR-3126-3p	CLIP-seq
MIRT1184239	hsa-miR-3150b-3p	CLIP-seq
MIRT1184240	hsa-miR-3652	CLIP-seq
MIRT1184241	hsa-miR-3921	CLIP-seq
MIRT1184242	hsa-miR-4283	CLIP-seq
MIRT1184243	hsa-miR-4311	CLIP-seq
MIRT1184244	hsa-miR-4430	CLIP-seq
MIRT1184245	hsa-miR-4433	CLIP-seq
MIRT1184246	hsa-miR-4489	CLIP-seq
MIRT1184247	hsa-miR-4492	CLIP-seq
MIRT1184248	hsa-miR-4498	CLIP-seq
MIRT1184249	hsa-miR-4505	CLIP-seq
MIRT1184250	hsa-miR-4649-3p	CLIP-seq
MIRT1184251	hsa-miR-4653-5p	CLIP-seq
MIRT1184252	hsa-miR-4667-5p	CLIP-seq
MIRT1184253	hsa-miR-4689	CLIP-seq
MIRT1184254	hsa-miR-4700-5p	CLIP-seq
MIRT1184255	hsa-miR-4784	CLIP-seq
MIRT1184256	hsa-miR-4794	CLIP-seq
MIRT1184257	hsa-miR-4795-5p	CLIP-seq
MIRT1184258	hsa-miR-593	CLIP-seq
MIRT1184259	hsa-miR-637	CLIP-seq
MIRT1184260	hsa-miR-661	CLIP-seq
MIRT1184261	hsa-miR-665	CLIP-seq
MIRT1184262	hsa-miR-762	CLIP-seq
MIRT2053440	hsa-miR-3122	CLIP-seq
MIRT2053441	hsa-miR-34c-3p	CLIP-seq
MIRT2053442	hsa-miR-3689a-3p	CLIP-seq
MIRT2053443	hsa-miR-3689c	CLIP-seq
MIRT2053444	hsa-miR-3913-5p	CLIP-seq
MIRT1184245	hsa-miR-4433	CLIP-seq
MIRT2053445	hsa-miR-4728-5p	CLIP-seq
MIRT2053446	hsa-miR-541	CLIP-seq
MIRT2053447	hsa-miR-654-5p	CLIP-seq
MIRT1184261	hsa-miR-665	CLIP-seq
MIRT2282648	hsa-miR-1285	CLIP-seq
MIRT2282649	hsa-miR-214	CLIP-seq
MIRT2053440	hsa-miR-3122	CLIP-seq
MIRT2282650	hsa-miR-3187-5p	CLIP-seq
MIRT2053441	hsa-miR-34c-3p	CLIP-seq
MIRT2282651	hsa-miR-3619-5p	CLIP-seq
MIRT2053442	hsa-miR-3689a-3p	CLIP-seq
MIRT2053443	hsa-miR-3689c	CLIP-seq
MIRT2282652	hsa-miR-3691-3p	CLIP-seq
MIRT2282653	hsa-miR-3913-3p	CLIP-seq
MIRT2053444	hsa-miR-3913-5p	CLIP-seq
MIRT2282654	hsa-miR-4291	CLIP-seq
MIRT1184243	hsa-miR-4311	CLIP-seq
MIRT1184245	hsa-miR-4433	CLIP-seq
MIRT2282655	hsa-miR-4436a	CLIP-seq
MIRT2053445	hsa-miR-4728-5p	CLIP-seq
MIRT2282656	hsa-miR-489	CLIP-seq
MIRT2282657	hsa-miR-516a-5p	CLIP-seq
MIRT2053446	hsa-miR-541	CLIP-seq
MIRT2282658	hsa-miR-612	CLIP-seq
MIRT2282659	hsa-miR-646	CLIP-seq
MIRT2053447	hsa-miR-654-5p	CLIP-seq
MIRT1184260	hsa-miR-661	CLIP-seq
MIRT1184261	hsa-miR-665	CLIP-seq
MIRT2282660	hsa-miR-761	CLIP-seq
MIRT2282661	hsa-miR-922	CLIP-seq
MIRT2455135	hsa-miR-3145-3p	CLIP-seq
MIRT2455136	hsa-miR-3173-3p	CLIP-seq
MIRT2455137	hsa-miR-3612	CLIP-seq
MIRT2455138	hsa-miR-4428	CLIP-seq
MIRT2455139	hsa-miR-4695-5p	CLIP-seq
MIRT2455140	hsa-miR-650	CLIP-seq
MIRT2053440	hsa-miR-3122	CLIP-seq
MIRT2053442	hsa-miR-3689a-3p	CLIP-seq
MIRT2053443	hsa-miR-3689c	CLIP-seq
MIRT2053444	hsa-miR-3913-5p	CLIP-seq
MIRT2053445	hsa-miR-4728-5p	CLIP-seq
MIRT2053446	hsa-miR-541	CLIP-seq
MIRT2053447	hsa-miR-654-5p	CLIP-seq
MIRT2053440	hsa-miR-3122	CLIP-seq
MIRT2053442	hsa-miR-3689a-3p	CLIP-seq
MIRT2053443	hsa-miR-3689c	CLIP-seq
MIRT2053444	hsa-miR-3913-5p	CLIP-seq
MIRT2053445	hsa-miR-4728-5p	CLIP-seq
MIRT2053446	hsa-miR-541	CLIP-seq
MIRT2053447	hsa-miR-654-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001650	Component	Fibrillar center	IDA
GO:0005515	Function	Protein binding	IPI	16439205, 18064046, 21349273, 24095731, 29997244
GO:0005634	Component	Nucleus	IDA	16439204, 16439205
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0006303	Process	Double-strand break repair via nonhomologous end joining	IBA	21873635
GO:0006303	Process	Double-strand break repair via nonhomologous end joining	IMP	16439204, 16439205
GO:0006303	Process	Double-strand break repair via nonhomologous end joining	TAS
GO:0007417	Process	Central nervous system development	NAS	16439204
GO:0010212	Process	Response to ionizing radiation	IDA	16439205
GO:0030183	Process	B cell differentiation	IMP	16439204
GO:0030217	Process	T cell differentiation	IMP	16439204
GO:0032807	Component	DNA ligase IV complex	IBA	21873635
GO:0045027	Function	DNA end binding	IBA	21873635
GO:0051351	Process	Positive regulation of ligase activity	NAS	16439205
GO:0070419	Component	Nonhomologous end joining complex	IBA	21873635
GO:0070419	Component	Nonhomologous end joining complex	IDA	20383123, 25941166

Other IDs

• MIM: 611290
• HGNC: 25737
• e!Ensembl: ENSG00000187736

Protein

• UniProt ID: Q9H9Q4
• Protein name: Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)
• Protein function: DNA repair protein involved in DNA non-homologous end joining (NHEJ); it is required for double-strand break (DSB) repair and V(D)J recombination and is also involved in telomere maintenance (PubMed:16439204, PubMed:16439205, PubMed:17317666, Pu
• PDB: 2QM4, 2R9A, 3Q4F, 3RWR, 3SR2, 3W03, 6ERG, 6ERH, 7LSY, 7LT3, 7NFC, 7NFE, 7ZYG, 8BHV, 8BHY, 8BOT, 8EZA, 8EZB
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF09302	XLF	12 → 182	XLF-Cernunnos, XRcc4-like factor, NHEJ component	Family

• Sequence:

  MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKE
  LNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWN
  FHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLK
  TEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQEVQVGQKHQGAGDPHT
  SNSASLQGIDSQCVNQPEQLVSSAPTLSAPEKESTGTSGPLQRPQLSKVKRKKPRGLFS

• Sequence length: 299

Pathways

KEGG:

Non-homologous end-joining

Reactome:

Nonhomologous End-Joining (NHEJ)

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Anemia	Anemia	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
Microcephaly	Microcephaly	rs397704721, rs267607176, rs267607177, rs397704725, rs267606717, rs267606718, rs199422202, rs121434311, rs199422203, rs199422126, rs387906274, rs121434305, rs199422125, rs199422135, rs189678019, rs199422184, rs137852994, rs137852995, rs137852996, rs137852997, rs145489194, rs80338860, rs137852494, rs121918609, rs199422207, rs199422206, rs29001566, rs864321658, rs199422138, rs199422139, rs199422141, rs199422144, rs199422147, rs199422151, rs199422152, rs199422153, rs199422157, rs199422159, rs199422160, rs199422161, rs140602858, rs199422164, rs199422165, rs148294838, rs199422134, rs199422168, rs199422172, rs199422173, rs199422131, rs199422177, rs199422180, rs199422185, rs199422186, rs199422187, rs143931757, rs199422189, rs199422192, rs199422194, rs199422195, rs199422196, rs199422197, rs199422199, rs753597039, rs1488084787, rs387906961, rs755862917, rs387907082, rs587776899, rs387907083, rs587776900, rs587776901, rs387907084, rs863223322, rs764201220, rs202247811, rs763915472, rs587776986, rs587777036, rs398122971, rs374351172, rs373278668, rs398122976, rs121909123, rs587783393, rs730882076, rs587783211, rs144716013, rs606231255, rs587783215, rs587783216, rs587783220, rs587783221, rs587783225, rs587783227, rs587783228, rs587783230, rs587783238, rs587783239, rs587783240, rs587783245, rs587783247, rs587783248, rs587783258, rs587783259, rs587783263, rs587783265, rs587783268, rs587783269, rs587783272, rs587783275, rs587783277, rs587783278, rs587783280, rs587783282, rs587783283, rs587783285, rs587783287, rs587783288, rs587783289, rs587783292, rs587783295, rs587784452, rs587783741, rs587783735, rs587783392, rs587783390, rs587783387, rs587783410, rs202058504, rs587783423, rs587783421, rs587783414, rs587784553, rs587784558, rs587784546, rs587784549, rs587784554, rs587784412, rs876661307, rs869025200, rs747831095, rs748529285, rs797045316, rs797045315, rs797045314, rs759632528, rs797045313, rs797045311, rs754282058, rs797045441, rs797045454, rs797045430, rs869312853, rs797046109, rs767399782, rs863225127, rs863225464, rs863225465, rs780270096, rs864321621, rs864321620, rs775277800, rs879253817, rs869312824, rs761447719, rs753406334, rs147622433, rs199422137, rs879255522, rs879255524, rs879255523, rs886037892, rs886037893, rs886037894, rs886037895, rs199422169, rs886041709, rs886041282, rs138228629, rs759188041, rs769688376, rs1057517688, rs1057519087, rs1057518268, rs933106143, rs201362977, rs754909135, rs1057520873, rs1060499758, rs1060499757, rs199422146, rs748016594, rs1085307120, rs763715733, rs1064795945, rs763800571, rs1554728351, rs1553227021, rs555866170, rs1553895368, rs1334947797, rs769818500, rs1321892596, rs1553227645, rs1404276011, rs1553228275, rs1554471681, rs1554496609, rs1555420891, rs1555418825, rs587784548, rs1555723585, rs199736219, rs745997770, rs765275884, rs1553924800, rs1554730137, rs1229568621, rs1482100822, rs979186313, rs758157294, rs1555294652, rs1555299107, rs1553264033, rs1553259539, rs1553254322, rs1553259528, rs981349334, rs1553264036, rs1553253022, rs754267846, rs776034810, rs1342429887, rs752140135, rs1006898944, rs571640983, rs1477524771, rs763909256, rs199910503, rs1553223496, rs759663956, rs1553446603, rs1555139372, rs1555143325, rs1350194762, rs1555141158, rs1553225179, rs769481947, rs769364943, rs748011724, rs1334301723, rs746341112, rs149225624, rs765113367, rs1567024512, rs142865061, rs772050241, rs201721894, rs1557966012, rs1379578836, rs1568334868, rs1185537869, rs1602333390, rs1163303148, rs774338373, rs770540184, rs1571600045, rs1571601267, rs1571602991, rs1588472215, rs1599841026, rs1558328287, rs1571600860, rs1571596976, rs1309880692, rs1435239428, rs1588634016, rs1751797979, rs1810830776, rs1815354949, rs1949984655, rs886039658, rs1943461045, rs777711720, rs2031759596, rs1555710223, rs1221031683, rs774069989, rs2058919680, rs1170413397, rs1213710245, rs1599851667, rs1599760058, rs1971033478, rs746967357
Severe combined immunodeficiency disease	Combined immunodeficiency	rs886037607, rs118203993, rs121908714, rs121908739, rs121908740, rs121908735, rs121908721, rs121908722, rs121908156, rs1564414523, rs1564418254, rs1564446526, rs786205074, rs121908157, rs121908159, rs786200884, rs397515357, rs104894562, rs137852624, rs137852625, rs137852626, rs137852627, rs137852507, rs137852509, rs111033619, rs111033620, rs1569480018, rs111033621, rs137852510, rs587776729, rs111033622, rs111033617, rs111033618, rs121917894, rs121917896, rs2133313409, rs121917897, rs28933392, rs104894282, rs104894283, rs104894285, rs121918570, rs121918572, rs730880318, rs104893674, rs730880319, rs104894453, rs104894454, rs104894451, rs137853206, rs777503956, rs267606645, rs267606648, rs397515390, rs193922346, rs193922347, rs193922348, rs193922349, rs193922350, rs137852508, rs193922640, rs193922641, rs193922643, rs193922645, rs193922361, rs193922364, rs193922464, rs148508754, rs193922574, rs113994174, rs606231246, rs397514671, rs397514686, rs397514755, rs199474679, rs199474685, rs199474686, rs199474681, rs150739647, rs267605358, rs886041036, rs587777335, rs587778405, rs145092287, rs587777562, rs606231256, rs200296680, rs786205456, rs786205517, rs774202259, rs786205615, rs878853261, rs786205890, rs782753385, rs746052951, rs869025224, rs869312857, rs869320660, rs869320659, rs869320658, rs879253742, rs886037924, rs886037925, rs750610248, rs886039394, rs761242509, rs886039387, rs886041043, rs886041044, rs886042051, rs886041333, rs749481781, rs1057517747, rs1057519506, rs1057523762, rs1057521062, rs1057520644, rs761583890, rs751635016, rs55729925, rs1064793248, rs1064793347, rs1064794027, rs781410769, rs1555524788, rs1486760100, rs769633203, rs1556330713, rs1555322558, rs1556330234, rs1556330755, rs1556329779, rs1556330552, rs1556329822, rs1556330286, rs1556331272, rs2146178281, rs376610445, rs757797994, rs775704953, rs1555743321, rs1564995660, rs1564995662, rs1556330249, rs144104577, rs886041796, rs1026474882, rs570768621, rs1556330562, rs1556330568, rs780014431, rs778343059, rs1555844617, rs1567629968, rs1567628757, rs1567629943, rs1567632864, rs1567632829, rs1567626023, rs1559328006, rs1561423197, rs1452483770, rs1568400897, rs1569479913, rs1568404443, rs1569480047, rs1563340753, rs368303189, rs1568431262, rs1568431102, rs1561424886, rs1602289943, rs1241698978, rs1569479994, rs1569480082, rs1602289649, rs1573261820, rs770985198, rs1589050343, rs1340132582, rs1589064324, rs1589070600, rs1213680890, rs149316157, rs1599873591, rs755706305, rs1602288051, rs1602289411, rs1602289183, rs1583513256, rs1589136659, rs1380154594, rs1011307501, rs1599876167, rs1569967422, rs1602289631, rs1573262398, rs760191638, rs1592117677, rs1640406042, rs372597855, rs1839558393, rs1839622622, rs1839957089, rs777008519, rs1233957241, rs2092261618, rs1839255008, rs1677695565, rs936493226, rs1162344514, rs991089005
Severe combined immunodeficiency with microcephaly, growth retardation, and sensitivity to ionizing radiation	Cernunnos-XLF deficiency, Severe Combined Immunodeficiency with Microcephaly, Growth Retardation, and Sensitivity to Ionizing Radiation	rs118204452, rs118204453, rs886037606, rs886037607, rs1064793763, rs1553542017, rs1949865586, rs753495484	17317666, 16439205, 16439204

Unknown
Disease name	Disease term	dbSNP ID	References
Immunologic deficiency syndromes	Immunologic Deficiency Syndromes