Incidental Mutation 'R3693:Nfxl1'
ID 268853
Institutional Source Beutler Lab
Gene Symbol Nfxl1
Ensembl Gene ENSMUSG00000072889
Gene Name nuclear transcription factor, X-box binding-like 1
Synonyms D430033A06Rik, LOC381696, 1700012H24Rik, TCF9
MMRRC Submission 040688-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.144) question?
Stock # R3693 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 72670644-72717027 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 72697954 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 297 (Y297C)
Ref Sequence ENSEMBL: ENSMUSP00000084467 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000074948] [ENSMUST00000087216] [ENSMUST00000135318]
AlphaFold E9Q8I7
Predicted Effect probably damaging
Transcript: ENSMUST00000074948
AA Change: Y297C

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000074481
Gene: ENSMUSG00000072889
AA Change: Y297C

DomainStartEndE-ValueType
low complexity region 9 19 N/A INTRINSIC
low complexity region 25 64 N/A INTRINSIC
low complexity region 106 125 N/A INTRINSIC
low complexity region 134 142 N/A INTRINSIC
RING 167 226 4.99e-1 SMART
ZnF_NFX 272 290 2.83e-3 SMART
ZnF_NFX 325 344 1.42e-3 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000087216
AA Change: Y297C

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000084467
Gene: ENSMUSG00000072889
AA Change: Y297C

DomainStartEndE-ValueType
low complexity region 9 19 N/A INTRINSIC
low complexity region 25 64 N/A INTRINSIC
low complexity region 106 125 N/A INTRINSIC
low complexity region 134 142 N/A INTRINSIC
RING 167 226 4.99e-1 SMART
ZnF_NFX 272 290 2.83e-3 SMART
ZnF_NFX 325 344 1.42e-3 SMART
ZnF_NFX 378 397 2.88e-4 SMART
ZnF_NFX 431 450 5.01e-4 SMART
ZnF_NFX 458 479 1.67e2 SMART
ZnF_NFX 483 502 9.71e-2 SMART
ZnF_NFX 510 529 3.49e-3 SMART
ZnF_NFX 567 587 4.56e1 SMART
Pfam:zf-NF-X1 596 608 6.8e-3 PFAM
ZnF_NFX 677 710 4.23e1 SMART
ZnF_NFX 720 738 5.49e-1 SMART
ZnF_NFX 782 801 1.63e-3 SMART
coiled coil region 829 880 N/A INTRINSIC
transmembrane domain 897 914 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000135318
AA Change: Y297C

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000114355
Gene: ENSMUSG00000072889
AA Change: Y297C

DomainStartEndE-ValueType
low complexity region 9 19 N/A INTRINSIC
low complexity region 25 64 N/A INTRINSIC
low complexity region 106 125 N/A INTRINSIC
low complexity region 134 142 N/A INTRINSIC
RING 167 226 4.99e-1 SMART
ZnF_NFX 272 290 2.83e-3 SMART
ZnF_NFX 325 344 1.42e-3 SMART
ZnF_NFX 378 397 2.88e-4 SMART
ZnF_NFX 431 450 5.01e-4 SMART
ZnF_NFX 458 479 1.67e2 SMART
Meta Mutation Damage Score 0.1687 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 97.2%
  • 20x: 94.9%
Validation Efficiency 97% (37/38)
Allele List at MGI
Other mutations in this stock
Total: 36 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2010106E10Rik A T X: 111,466,012 (GRCm39) L187F probably damaging Het
Ankrd29 G A 18: 12,387,757 (GRCm39) A275V possibly damaging Het
Cabp2 A G 19: 4,133,593 (GRCm39) T12A probably benign Het
Ccdc158 T C 5: 92,757,904 (GRCm39) E1056G probably damaging Het
Cdhr2 A G 13: 54,874,229 (GRCm39) Y767C probably damaging Het
Ces2e A G 8: 105,655,443 (GRCm39) D122G probably damaging Het
Cherp TTGCTGCTGCTGCTGCTGCTG TTGCTGCTGCTGCTGCTG 8: 73,221,755 (GRCm39) probably benign Het
Chsy3 A T 18: 59,309,080 (GRCm39) Q111L possibly damaging Het
Crygs C T 16: 22,624,301 (GRCm39) G102D possibly damaging Het
Cyp11b2 C T 15: 74,727,857 (GRCm39) R75Q probably benign Het
Dnaja2 T C 8: 86,273,249 (GRCm39) K223E probably damaging Het
Dtx3 T C 10: 127,027,293 (GRCm39) I294V probably benign Het
Eps15l1 A G 8: 73,152,904 (GRCm39) probably benign Het
Exd2 A G 12: 80,527,467 (GRCm39) Y220C probably damaging Het
Eya1 A G 1: 14,299,725 (GRCm39) Y343H probably damaging Het
Hif3a T C 7: 16,774,999 (GRCm39) E533G probably damaging Het
Kalrn T A 16: 34,177,685 (GRCm39) Y178F probably damaging Het
Mageb4 G T X: 85,296,000 (GRCm39) R10S probably damaging Het
Muc6 A G 7: 141,234,946 (GRCm39) probably benign Het
Myh11 C A 16: 14,035,813 (GRCm39) E1038D probably benign Het
Nop14 T C 5: 34,811,782 (GRCm39) K202E probably damaging Het
Or5b112 T C 19: 13,319,893 (GRCm39) I257T possibly damaging Het
Osbpl8 T A 10: 111,105,297 (GRCm39) S251T probably benign Het
Pcdha1 A T 18: 37,065,361 (GRCm39) K675I possibly damaging Het
Pigw A G 11: 84,769,209 (GRCm39) I40T probably benign Het
Pip5k1a A T 3: 94,985,498 (GRCm39) probably benign Het
Ptprh G T 7: 4,557,234 (GRCm39) Q687K probably damaging Het
Rbm4 A G 19: 4,837,411 (GRCm39) Y358H probably damaging Het
Rft1 T A 14: 30,412,408 (GRCm39) C490S probably damaging Het
Rims2 A T 15: 39,341,971 (GRCm39) T887S probably benign Het
Ripk2 A T 4: 16,127,695 (GRCm39) L349Q probably benign Het
Strn T C 17: 78,964,421 (GRCm39) N515D probably damaging Het
Stxbp5l A T 16: 37,061,708 (GRCm39) Y367* probably null Het
Tas2r143 G A 6: 42,377,910 (GRCm39) V247I probably benign Het
Togaram1 A T 12: 65,030,283 (GRCm39) Y1029F probably benign Het
Ugt1a6b A G 1: 88,035,516 (GRCm39) T285A probably benign Het
Other mutations in Nfxl1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01094:Nfxl1 APN 5 72,707,771 (GRCm39) splice site probably benign
IGL01716:Nfxl1 APN 5 72,698,277 (GRCm39) missense probably damaging 1.00
IGL02592:Nfxl1 APN 5 72,671,572 (GRCm39) missense probably benign 0.25
IGL03083:Nfxl1 APN 5 72,698,005 (GRCm39) splice site probably benign
FR4548:Nfxl1 UTSW 5 72,716,458 (GRCm39) small insertion probably benign
FR4737:Nfxl1 UTSW 5 72,716,464 (GRCm39) small insertion probably benign
R0478:Nfxl1 UTSW 5 72,681,988 (GRCm39) critical splice donor site probably null
R0725:Nfxl1 UTSW 5 72,716,473 (GRCm39) missense probably benign
R1374:Nfxl1 UTSW 5 72,681,488 (GRCm39) missense probably benign 0.04
R1616:Nfxl1 UTSW 5 72,686,380 (GRCm39) missense probably benign 0.01
R1752:Nfxl1 UTSW 5 72,698,218 (GRCm39) missense probably damaging 1.00
R2108:Nfxl1 UTSW 5 72,671,675 (GRCm39) critical splice acceptor site probably null
R3081:Nfxl1 UTSW 5 72,686,378 (GRCm39) missense possibly damaging 0.92
R3725:Nfxl1 UTSW 5 72,674,405 (GRCm39) missense probably damaging 1.00
R4660:Nfxl1 UTSW 5 72,710,011 (GRCm39) missense probably damaging 1.00
R5058:Nfxl1 UTSW 5 72,713,582 (GRCm39) missense probably benign 0.03
R5406:Nfxl1 UTSW 5 72,713,541 (GRCm39) missense possibly damaging 0.92
R5447:Nfxl1 UTSW 5 72,686,512 (GRCm39) missense probably benign 0.01
R5634:Nfxl1 UTSW 5 72,686,833 (GRCm39) missense probably damaging 1.00
R5831:Nfxl1 UTSW 5 72,679,540 (GRCm39) missense probably benign
R5910:Nfxl1 UTSW 5 72,697,708 (GRCm39) missense probably benign 0.05
R6086:Nfxl1 UTSW 5 72,698,362 (GRCm39) missense probably benign 0.39
R6091:Nfxl1 UTSW 5 72,671,533 (GRCm39) missense probably benign 0.00
R6212:Nfxl1 UTSW 5 72,673,553 (GRCm39) critical splice donor site probably null
R6501:Nfxl1 UTSW 5 72,685,852 (GRCm39) splice site probably null
R6521:Nfxl1 UTSW 5 72,697,651 (GRCm39) splice site probably null
R7283:Nfxl1 UTSW 5 72,686,393 (GRCm39) missense probably benign
R7426:Nfxl1 UTSW 5 72,681,517 (GRCm39) nonsense probably null
R7480:Nfxl1 UTSW 5 72,716,595 (GRCm39) nonsense probably null
R7648:Nfxl1 UTSW 5 72,680,879 (GRCm39) missense probably benign 0.12
R7817:Nfxl1 UTSW 5 72,671,632 (GRCm39) missense possibly damaging 0.89
R7899:Nfxl1 UTSW 5 72,681,558 (GRCm39) missense probably damaging 1.00
R8186:Nfxl1 UTSW 5 72,716,355 (GRCm39) critical splice donor site probably null
R8468:Nfxl1 UTSW 5 72,675,548 (GRCm39) missense possibly damaging 0.95
R8765:Nfxl1 UTSW 5 72,686,443 (GRCm39) missense probably benign
R8969:Nfxl1 UTSW 5 72,716,473 (GRCm39) missense unknown
R9330:Nfxl1 UTSW 5 72,681,451 (GRCm39) missense probably benign 0.00
R9385:Nfxl1 UTSW 5 72,694,750 (GRCm39) missense probably benign 0.13
R9419:Nfxl1 UTSW 5 72,716,641 (GRCm39) intron probably benign
R9496:Nfxl1 UTSW 5 72,685,502 (GRCm39) missense possibly damaging 0.81
Z1176:Nfxl1 UTSW 5 72,695,493 (GRCm39) missense probably null 0.89
Predicted Primers PCR Primer
(F):5'- GGACAAGGCTGACAGTTTCC -3'
(R):5'- GTTTGCCGTGAGACAATGGAG -3'

Sequencing Primer
(F):5'- CAAGGCTGACAGTTTCCTAAAATTAC -3'
(R):5'- TGAGACAATGGAGAAAGGTTTACCC -3'
Posted On 2015-02-19