Incidental Mutation 'R5918:Nr6a1'
ID 461443
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 044115-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5918 (G1)
Quality Score 218
Status Validated
Chromosome 2
Chromosomal Location 38613381-38816473 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 38629103 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 250 (D250G)
Ref Sequence ENSEMBL: ENSMUSP00000126009 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000076275] [ENSMUST00000112877] [ENSMUST00000142113] [ENSMUST00000168098] [ENSMUST00000142130]
AlphaFold Q64249
Predicted Effect probably damaging
Transcript: ENSMUST00000076275
AA Change: D307G

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000075624
Gene: ENSMUSG00000063972
AA Change: D307G

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: D307G

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000108498
Gene: ENSMUSG00000063972
AA Change: D307G

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 noncoding transcript
Transcript: ENSMUST00000123342
Predicted Effect noncoding transcript
Transcript: ENSMUST00000128688
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132636
Predicted Effect probably benign
Transcript: ENSMUST00000142113
SMART Domains Protein: ENSMUSP00000121234
Gene: ENSMUSG00000063972

DomainStartEndE-ValueType
ZnF_C4 15 86 9.35e-36 SMART
Blast:HOLI 105 235 6e-67 BLAST
Predicted Effect probably damaging
Transcript: ENSMUST00000168098
AA Change: D250G

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000126009
Gene: ENSMUSG00000063972
AA Change: D250G

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156301
Predicted Effect noncoding transcript
Transcript: ENSMUST00000203202
Predicted Effect probably benign
Transcript: ENSMUST00000142130
SMART Domains Protein: ENSMUSP00000115164
Gene: ENSMUSG00000063972

DomainStartEndE-ValueType
low complexity region 23 31 N/A INTRINSIC
ZnF_C4 57 128 9.35e-36 SMART
low complexity region 187 201 N/A INTRINSIC
Meta Mutation Damage Score 0.9745 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.8%
  • 20x: 93.6%
Validation Efficiency 93% (66/71)
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: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Afap1 A T 5: 36,131,869 (GRCm39) I399F possibly damaging Het
Aknad1 C T 3: 108,659,703 (GRCm39) P239L probably benign Het
Ankrd9 A G 12: 110,943,200 (GRCm39) V245A probably benign Het
Anxa1 T C 19: 20,355,857 (GRCm39) probably benign Het
Arhgef2 A G 3: 88,543,387 (GRCm39) K454R probably damaging Het
AU040320 A G 4: 126,708,064 (GRCm39) T227A probably benign Het
Bbs2 C T 8: 94,824,931 (GRCm39) R17H probably damaging Het
Bcl2l12 A G 7: 44,640,888 (GRCm39) probably benign Het
C1qtnf9 G T 14: 61,009,737 (GRCm39) probably benign Het
Ccdc38 C G 10: 93,406,748 (GRCm39) Y219* probably null Het
Ceacam3 G T 7: 16,893,670 (GRCm39) D394Y probably damaging Het
Crip1 A C 12: 113,117,287 (GRCm39) probably null Het
Dnah7b T C 1: 46,260,803 (GRCm39) V1987A probably benign Het
Dnah9 C A 11: 65,725,025 (GRCm39) C4376F probably damaging Het
Galnt9 T C 5: 110,763,332 (GRCm39) F446L probably damaging Het
Garin1a A G 6: 29,285,942 (GRCm39) R76G probably null Het
Gm14322 A G 2: 177,411,499 (GRCm39) D103G probably benign Het
Gpa33 T C 1: 165,958,107 (GRCm39) probably null Het
Lactb2 T A 1: 13,720,954 (GRCm39) I93F probably benign Het
Lifr A T 15: 7,188,897 (GRCm39) T93S probably benign Het
Lmbr1l A T 15: 98,810,308 (GRCm39) I101N probably damaging Het
Lrrc8c G A 5: 105,756,117 (GRCm39) V631M possibly damaging Het
Mctp2 A C 7: 71,878,288 (GRCm39) D263E probably damaging Het
Nbeal1 T A 1: 60,307,051 (GRCm39) I1627N possibly damaging Het
Neb T C 2: 52,087,906 (GRCm39) Y5188C probably damaging Het
Nf1 T C 11: 79,460,048 (GRCm39) probably benign Het
Ola1 T C 2: 72,987,128 (GRCm39) E168G probably benign Het
Or1a1 T C 11: 74,086,944 (GRCm39) V205A probably damaging Het
Or2d2b T A 7: 106,705,828 (GRCm39) Q80L probably damaging Het
Or4k2 A G 14: 50,424,425 (GRCm39) I83T probably benign Het
Or7g22 T C 9: 19,048,684 (GRCm39) Y132H probably damaging Het
Or9i1b T A 19: 13,897,139 (GRCm39) F252I probably damaging Het
Pik3r6 C T 11: 68,416,497 (GRCm39) Q29* probably null Het
Ppargc1a C T 5: 51,620,579 (GRCm39) probably benign Het
Ppl C T 16: 4,922,765 (GRCm39) R242H probably benign Het
Ppp1r37 G T 7: 19,266,036 (GRCm39) Q577K probably benign Het
Prcd A G 11: 116,548,366 (GRCm39) E25G probably damaging Het
Prpsap2 C T 11: 61,627,870 (GRCm39) R202H probably damaging Het
Ptgs1 A C 2: 36,141,089 (GRCm39) E512A probably damaging Het
Radil T G 5: 142,473,357 (GRCm39) I535L probably benign Het
Rbl2 G T 8: 91,816,758 (GRCm39) V373F probably benign Het
Ryr1 T C 7: 28,708,577 (GRCm39) Y4802C probably benign Het
Sdc2 A G 15: 33,028,313 (GRCm39) T144A probably benign Het
Senp6 T C 9: 80,021,398 (GRCm39) probably null Het
Sipa1l3 T C 7: 29,096,631 (GRCm39) D531G probably damaging Het
Slc22a27 C A 19: 7,887,411 (GRCm39) C189F possibly damaging Het
Srcin1 T C 11: 97,424,323 (GRCm39) probably null Het
Svep1 C T 4: 58,069,345 (GRCm39) E2814K possibly damaging Het
Tjp3 T G 10: 81,113,746 (GRCm39) H504P probably benign Het
Tmprss4 T A 9: 45,086,414 (GRCm39) K378* probably null Het
Tns4 C T 11: 98,964,497 (GRCm39) probably null Het
Ttn T C 2: 76,580,298 (GRCm39) T15205A possibly damaging Het
Ush2a G T 1: 188,089,011 (GRCm39) G322V probably benign Het
Vac14 A T 8: 111,363,104 (GRCm39) probably null Het
Vmn1r175 T G 7: 23,508,372 (GRCm39) D85A probably damaging Het
Vmn2r93 T C 17: 18,546,030 (GRCm39) L634P probably damaging Het
Zeb2 A T 2: 45,001,271 (GRCm39) probably benign Het
Zfp616 T A 11: 73,974,086 (GRCm39) H118Q possibly damaging Het
Zfp945 T A 17: 23,069,955 (GRCm39) H648L probably damaging Het
Zscan29 G T 2: 120,994,518 (GRCm39) T489N probably 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
R6210:Nr6a1 UTSW 2 38,619,509 (GRCm39) missense probably damaging 0.99
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'- CTTGCTTAGTCCAGATCGCC -3'
(R):5'- ATCTGTGGTCAAGGGCAAG -3'

Sequencing Primer
(F):5'- CACCTGTGGAGTTCTTCATCAGAG -3'
(R):5'- GAGGCCTACTACCAAGGAATCCTTC -3'
Posted On 2017-02-28