Incidental Mutation 'R6210:Nr6a1'
ID 503380
Institutional Source Beutler Lab
Gene Symbol Nr6a1
Ensembl Gene ENSMUSG00000063972
Gene Name nuclear receptor subfamily 6, group A, member 1
Synonyms 1700113M01Rik, NCNF, Gcnf
MMRRC Submission 044344-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6210 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 38613381-38816473 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 38619509 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Serine at position 462 (I462S)
Ref Sequence ENSEMBL: ENSMUSP00000108498 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000076275] [ENSMUST00000112877] [ENSMUST00000168098]
AlphaFold Q64249
Predicted Effect probably damaging
Transcript: ENSMUST00000076275
AA Change: I462S

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000075624
Gene: ENSMUSG00000063972
AA Change: I462S

DomainStartEndE-ValueType
low complexity region 23 31 N/A INTRINSIC
ZnF_C4 72 143 9.35e-36 SMART
low complexity region 202 216 N/A INTRINSIC
HOLI 304 466 3.19e-29 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000112877
AA Change: I462S

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000108498
Gene: ENSMUSG00000063972
AA Change: I462S

DomainStartEndE-ValueType
low complexity region 23 31 N/A INTRINSIC
ZnF_C4 72 143 9.35e-36 SMART
low complexity region 202 216 N/A INTRINSIC
HOLI 304 466 3.19e-29 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000168098
AA Change: I405S

PolyPhen 2 Score 0.925 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000126009
Gene: ENSMUSG00000063972
AA Change: I405S

DomainStartEndE-ValueType
ZnF_C4 15 86 9.35e-36 SMART
low complexity region 145 159 N/A INTRINSIC
HOLI 247 409 3.19e-29 SMART
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.5%
  • 20x: 98.4%
Validation Efficiency 95% (52/55)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an orphan nuclear receptor which is a member of the nuclear hormone receptor family. Its expression pattern suggests that it may be involved in neurogenesis and germ cell development. The protein can homodimerize and bind DNA, but in vivo targets have not been identified. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jun 2013]
PHENOTYPE: Homozygotes for targeted null mutations have cardiovascular abnormalities, defective trunk development, impaired somite formation, failure to turn, open neural tube and hindgut, protrusion of the tailbud outside the yolk sac and die by embryonic day 10.5. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abhd3 T A 18: 10,706,032 (GRCm39) I94F probably damaging Het
Bbox1 A T 2: 110,100,422 (GRCm39) D258E probably benign Het
Catsperb A G 12: 101,378,827 (GRCm39) probably null Het
Ccdc127 T C 13: 74,505,040 (GRCm39) V196A probably benign Het
Cd101 A T 3: 100,925,959 (GRCm39) D253E probably damaging Het
Ceacam15 T C 7: 16,407,214 (GRCm39) Y101C probably damaging Het
Cep135 C T 5: 76,772,570 (GRCm39) L652F probably benign Het
Col5a1 G T 2: 27,922,633 (GRCm39) V234L probably benign Het
Cxcr6 T C 9: 123,639,073 (GRCm39) S25P possibly damaging Het
Dctn4 C T 18: 60,679,865 (GRCm39) Q258* probably null Het
Fmnl2 A T 2: 53,020,457 (GRCm39) N1067I possibly damaging Het
Frrs1 A T 3: 116,672,080 (GRCm39) K59N probably benign Het
Gpr157 T C 4: 150,186,055 (GRCm39) Y206H probably damaging Het
Hephl1 A G 9: 15,001,860 (GRCm39) Y161H possibly damaging Het
Hinfp C T 9: 44,210,169 (GRCm39) probably null Het
Igf2r A T 17: 12,933,838 (GRCm39) N805K probably damaging Het
Ilrun A T 17: 27,986,960 (GRCm39) D255E probably benign Het
Itga3 T C 11: 94,959,717 (GRCm39) probably benign Het
Itga6 A G 2: 71,664,351 (GRCm39) probably null Het
Kcnip1 G A 11: 33,595,600 (GRCm39) T30I possibly damaging Het
Lig4 T C 8: 10,021,585 (GRCm39) T732A probably benign Het
Lmod3 T A 6: 97,224,262 (GRCm39) T520S probably damaging Het
Megf8 G A 7: 25,043,145 (GRCm39) V1356I possibly damaging Het
Mical3 C T 6: 121,017,478 (GRCm39) probably null Het
Msi1 T C 5: 115,573,535 (GRCm39) I8T probably damaging Het
Mug4-ps A T 6: 121,927,276 (GRCm39) noncoding transcript Het
Myo1f T A 17: 33,820,044 (GRCm39) I783N probably damaging Het
Or2t48 C T 11: 58,420,090 (GRCm39) A241T probably damaging Het
Or8k23 A G 2: 86,186,702 (GRCm39) V8A probably benign Het
Pah C A 10: 87,419,423 (GRCm39) Q449K probably benign Het
Pced1a A G 2: 130,263,839 (GRCm39) V271A probably damaging Het
Pdzrn4 A T 15: 92,655,562 (GRCm39) E485V probably damaging Het
Psg21 A G 7: 18,386,270 (GRCm39) Y239H probably damaging Het
Ptprt T C 2: 162,109,949 (GRCm39) Y180C probably damaging Het
Raet1d T A 10: 22,246,849 (GRCm39) I59N probably damaging Het
Rfx1 T C 8: 84,819,647 (GRCm39) L653P probably damaging Het
Rnase2a A G 14: 51,493,131 (GRCm39) V78A possibly damaging Het
Rsf1 ATGGCG ATGGCGACGGTGGCG 7: 97,229,111 (GRCm39) probably benign Homo
Serbp1 T C 6: 67,249,851 (GRCm39) probably benign Het
Tlr1 A T 5: 65,082,629 (GRCm39) H649Q probably damaging Het
Tns2 C T 15: 102,017,369 (GRCm39) R281C probably damaging Het
Trpc6 T A 9: 8,656,731 (GRCm39) D719E probably benign Het
Ttc21b A T 2: 66,066,698 (GRCm39) S318R probably benign Het
Ttn G A 2: 76,579,673 (GRCm39) T23740M probably damaging Het
Uhmk1 T C 1: 170,039,806 (GRCm39) Q187R probably damaging Het
Ung C T 5: 114,269,438 (GRCm39) A50V probably benign Het
Upk3bl C T 5: 136,088,674 (GRCm39) Q103* probably null Het
Usp17le C A 7: 104,418,350 (GRCm39) C264F probably damaging Het
Vmn2r105 T A 17: 20,448,758 (GRCm39) N140Y probably damaging Het
Vmn2r84 C T 10: 130,222,114 (GRCm39) C702Y probably damaging Het
Zfp709 TCGACG TCG 8: 72,644,552 (GRCm39) probably benign Het
Zfp748 G A 13: 67,688,923 (GRCm39) P779L possibly damaging Het
Other mutations in Nr6a1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01566:Nr6a1 APN 2 38,617,901 (GRCm39) missense probably benign 0.06
IGL02245:Nr6a1 APN 2 38,630,565 (GRCm39) missense probably benign 0.04
IGL03195:Nr6a1 APN 2 38,632,948 (GRCm39) missense probably damaging 1.00
R0270:Nr6a1 UTSW 2 38,629,032 (GRCm39) missense possibly damaging 0.75
R0909:Nr6a1 UTSW 2 38,775,218 (GRCm39) missense probably benign 0.11
R1737:Nr6a1 UTSW 2 38,628,955 (GRCm39) missense probably benign 0.04
R5918:Nr6a1 UTSW 2 38,629,103 (GRCm39) missense probably damaging 1.00
R6311:Nr6a1 UTSW 2 38,629,083 (GRCm39) missense possibly damaging 0.69
R6861:Nr6a1 UTSW 2 38,630,597 (GRCm39) missense possibly damaging 0.71
R6978:Nr6a1 UTSW 2 38,762,631 (GRCm39) missense probably benign
R7566:Nr6a1 UTSW 2 38,621,085 (GRCm39) missense possibly damaging 0.77
R8177:Nr6a1 UTSW 2 38,619,510 (GRCm39) missense probably benign 0.02
R8441:Nr6a1 UTSW 2 38,632,888 (GRCm39) missense probably benign 0.05
R8548:Nr6a1 UTSW 2 38,619,551 (GRCm39) missense probably damaging 1.00
R8548:Nr6a1 UTSW 2 38,619,550 (GRCm39) missense probably damaging 1.00
R8776:Nr6a1 UTSW 2 38,650,244 (GRCm39) missense probably damaging 1.00
R8776-TAIL:Nr6a1 UTSW 2 38,650,244 (GRCm39) missense probably damaging 1.00
R8933:Nr6a1 UTSW 2 38,650,400 (GRCm39) missense probably damaging 0.99
R8982:Nr6a1 UTSW 2 38,762,613 (GRCm39) missense probably benign 0.00
R9189:Nr6a1 UTSW 2 38,816,129 (GRCm39) critical splice donor site probably null
R9284:Nr6a1 UTSW 2 38,638,890 (GRCm39) missense probably damaging 1.00
R9505:Nr6a1 UTSW 2 38,630,485 (GRCm39) missense probably benign 0.24
Predicted Primers PCR Primer
(F):5'- GTTCAAGACACAGACACAGGCTG -3'
(R):5'- TTATAAATCTGATGCCACCGCC -3'

Sequencing Primer
(F):5'- AGACACAGGCTGCTCTCGTC -3'
(R):5'- CACAGCTGGAACAACTGA -3'
Posted On 2018-02-27