Incidental Mutation 'R5399:Rtl1'
ID 429897
Institutional Source Beutler Lab
Gene Symbol Rtl1
Ensembl Gene ENSMUSG00000085925
Gene Name retrotransposon Gaglike 1
Synonyms Mart1, Mar, Mor1
MMRRC Submission 042970-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5399 (G1)
Quality Score 225
Status Not validated
Chromosome 12
Chromosomal Location 109555627-109566764 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 109556736 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Glutamine at position 1701 (L1701Q)
Ref Sequence ENSEMBL: ENSMUSP00000115957 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000149046]
AlphaFold Q7M732
Predicted Effect noncoding transcript
Transcript: ENSMUST00000083592
Predicted Effect noncoding transcript
Transcript: ENSMUST00000093564
Predicted Effect noncoding transcript
Transcript: ENSMUST00000093568
Predicted Effect noncoding transcript
Transcript: ENSMUST00000093572
Predicted Effect noncoding transcript
Transcript: ENSMUST00000093625
Predicted Effect noncoding transcript
Transcript: ENSMUST00000102167
Predicted Effect noncoding transcript
Transcript: ENSMUST00000102358
Predicted Effect probably damaging
Transcript: ENSMUST00000149046
AA Change: L1701Q

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000115957
Gene: ENSMUSG00000085925
AA Change: L1701Q

DomainStartEndE-ValueType
low complexity region 19 30 N/A INTRINSIC
low complexity region 41 80 N/A INTRINSIC
internal_repeat_1 88 163 8.8e-50 PROSPERO
internal_repeat_1 176 251 8.8e-50 PROSPERO
low complexity region 332 361 N/A INTRINSIC
low complexity region 380 391 N/A INTRINSIC
low complexity region 393 408 N/A INTRINSIC
Pfam:DUF4939 432 538 1.6e-14 PFAM
Pfam:Retrotrans_gag 493 586 9.2e-13 PFAM
low complexity region 611 632 N/A INTRINSIC
Pfam:gag-asp_proteas 663 731 2.3e-15 PFAM
low complexity region 833 849 N/A INTRINSIC
low complexity region 878 892 N/A INTRINSIC
PDB:4OL8|E 988 1192 6e-17 PDB
Blast:CYCc 989 1158 5e-9 BLAST
SCOP:d1sig__ 1291 1443 2e-4 SMART
low complexity region 1733 1744 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000200030
Predicted Effect noncoding transcript
Transcript: ENSMUST00000157230
Predicted Effect noncoding transcript
Transcript: ENSMUST00000175468
Predicted Effect noncoding transcript
Transcript: ENSMUST00000175205
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.3%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a retrotransposon-derived, paternally expressed imprinted gene that is highly expressed at the late fetal stage in both the fetus and placenta. It has an overlapping maternally expressed antisense transcript, which contains several microRNAs targeting the transcripts of this gene through an RNA interference (RNAi) mechanism. This gene is essential for maintenance of the fetal capillaries. [provided by RefSeq, Jul 2009]
PHENOTYPE: Mice heterozygous for a paternally inherited knock-out allele exhibit fetal/neonatal lethality associated with underdevelopment of the placenta. Mice heteroygous for a maternally inherited knock-out allele exhibit neonatal lethality and decreased survival associated with placental overdevelopment. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
6820408C15Rik G T 2: 152,282,788 (GRCm39) L214F probably damaging Het
Abcb1b T C 5: 8,877,410 (GRCm39) S657P probably benign Het
Abcb5 T A 12: 118,875,234 (GRCm39) Y646F probably benign Het
Agl A T 3: 116,575,277 (GRCm39) L620Q probably damaging Het
Anapc15 C T 7: 101,547,810 (GRCm39) P68L probably damaging Het
Arhgap23 A G 11: 97,391,743 (GRCm39) N1420S probably damaging Het
Barx2 A G 9: 31,765,407 (GRCm39) probably null Het
Birc6 C A 17: 74,911,573 (GRCm39) S28R possibly damaging Het
Bmal2 T G 6: 146,724,159 (GRCm39) D350E probably damaging Het
Btbd19 G A 4: 116,980,957 (GRCm39) A104V probably damaging Het
Casp4 A T 9: 5,324,928 (GRCm39) K247* probably null Het
Ccdc196 A C 12: 78,244,227 (GRCm39) N60T probably damaging Het
Clk4 T C 11: 51,166,084 (GRCm39) Y17H probably damaging Het
Cntnap1 A G 11: 101,074,142 (GRCm39) Q722R probably benign Het
Col6a6 A G 9: 105,586,306 (GRCm39) V1905A possibly damaging Het
Csmd1 C A 8: 16,760,613 (GRCm39) G174V probably damaging Het
Cul1 T A 6: 47,462,018 (GRCm39) probably null Het
Cux1 T C 5: 136,281,458 (GRCm39) E568G possibly damaging Het
Dnaaf2 A G 12: 69,243,516 (GRCm39) I515T probably damaging Het
Fbn1 T C 2: 125,174,253 (GRCm39) I1868V possibly damaging Het
Fcgbp G T 7: 27,804,480 (GRCm39) V1863L probably benign Het
G2e3 T C 12: 51,403,977 (GRCm39) probably null Het
Gabrr2 T C 4: 33,071,458 (GRCm39) probably null Het
Gad1-ps G A 10: 99,281,009 (GRCm39) noncoding transcript Het
Gbgt1 C T 2: 28,393,230 (GRCm39) P106L probably damaging Het
Golga3 A G 5: 110,352,890 (GRCm39) E927G probably damaging Het
Hfm1 T A 5: 107,065,428 (GRCm39) I84F possibly damaging Het
Htt G T 5: 35,034,495 (GRCm39) D1989Y probably damaging Het
Ihh C T 1: 74,985,436 (GRCm39) A350T probably benign Het
Irx4 G C 13: 73,413,658 (GRCm39) A43P probably benign Het
Itk A G 11: 46,228,938 (GRCm39) V414A probably benign Het
Itsn2 A T 12: 4,703,535 (GRCm39) I744L probably benign Het
Kdm5b G A 1: 134,549,836 (GRCm39) probably null Het
Kif14 A G 1: 136,431,062 (GRCm39) D1153G probably benign Het
Morc3 A G 16: 93,659,427 (GRCm39) probably null Het
Mplkipl1 C T 19: 61,164,364 (GRCm39) G24R unknown Het
Msc A T 1: 14,825,780 (GRCm39) C65S probably benign Het
Mybpc1 A G 10: 88,358,876 (GRCm39) V343A probably damaging Het
Myo5c T C 9: 75,195,356 (GRCm39) I1218T possibly damaging Het
Mypn C T 10: 62,955,965 (GRCm39) V1163I probably benign Het
Obox3 A T 7: 15,360,213 (GRCm39) M152K probably benign Het
Or1e16 AGCGGTCGTAGGC AGC 11: 73,286,480 (GRCm39) probably null Het
Or2t47 A G 11: 58,442,969 (GRCm39) V32A probably benign Het
Or4c106 T A 2: 88,682,999 (GRCm39) L235H probably damaging Het
Or4c3 T A 2: 89,852,267 (GRCm39) T48S probably benign Het
Pcdhb21 G T 18: 37,648,772 (GRCm39) V634L probably benign Het
Ppp1r9b G A 11: 94,882,974 (GRCm39) A201T probably benign Het
Pramel25 T C 4: 143,521,602 (GRCm39) F406S probably benign Het
Prss23 A T 7: 89,159,174 (GRCm39) D298E probably benign Het
Rab4b A T 7: 26,875,587 (GRCm39) N31K probably benign Het
Ros1 A G 10: 51,967,040 (GRCm39) probably null Het
Rragb G A X: 151,923,550 (GRCm39) G24E probably damaging Het
Sbno1 T A 5: 124,530,804 (GRCm39) N831Y probably benign Het
Selp A G 1: 163,954,155 (GRCm39) K152E possibly damaging Het
Sema4b A G 7: 79,874,634 (GRCm39) T675A probably benign Het
Slc36a3 T C 11: 55,037,006 (GRCm39) I100V possibly damaging Het
Slco1a4 T A 6: 141,776,433 (GRCm39) I196F probably damaging Het
Spata13 G A 14: 60,984,990 (GRCm39) S828N probably benign Het
Stard13 A T 5: 150,971,266 (GRCm39) Y643* probably null Het
Tll1 T C 8: 64,538,522 (GRCm39) H374R probably damaging Het
Trmt10a T A 3: 137,853,265 (GRCm39) I42K probably damaging Het
Trmu A T 15: 85,780,609 (GRCm39) probably null Het
Trp53 T A 11: 69,479,372 (GRCm39) D183E probably benign Het
Ttc22 T G 4: 106,493,954 (GRCm39) F305V probably damaging Het
Unc13c A G 9: 73,656,970 (GRCm39) F1077S possibly damaging Het
Utrn T A 10: 12,516,727 (GRCm39) Q2289L probably damaging Het
Vmn1r65 C A 7: 6,011,809 (GRCm39) E142* probably null Het
Vmn2r63 A T 7: 42,577,701 (GRCm39) V279D probably benign Het
Zfp810 G A 9: 22,190,125 (GRCm39) T261I possibly damaging Het
Zkscan17 A G 11: 59,393,744 (GRCm39) probably null Het
Other mutations in Rtl1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00672:Rtl1 APN 12 109,559,434 (GRCm39) missense probably benign 0.00
IGL01981:Rtl1 APN 12 109,558,369 (GRCm39) missense possibly damaging 0.72
IGL02418:Rtl1 APN 12 109,556,883 (GRCm39) missense probably damaging 1.00
IGL03164:Rtl1 APN 12 109,559,367 (GRCm39) missense probably damaging 1.00
FR4304:Rtl1 UTSW 12 109,557,632 (GRCm39) small deletion probably benign
R0109:Rtl1 UTSW 12 109,561,841 (GRCm39) start gained probably benign
R0141:Rtl1 UTSW 12 109,559,382 (GRCm39) missense probably damaging 1.00
R0312:Rtl1 UTSW 12 109,556,661 (GRCm39) missense probably damaging 0.99
R0389:Rtl1 UTSW 12 109,556,797 (GRCm39) missense possibly damaging 0.77
R0390:Rtl1 UTSW 12 109,557,820 (GRCm39) missense unknown
R0548:Rtl1 UTSW 12 109,558,089 (GRCm39) missense probably damaging 0.98
R0561:Rtl1 UTSW 12 109,560,363 (GRCm39) missense probably damaging 0.99
R0624:Rtl1 UTSW 12 109,559,153 (GRCm39) missense probably damaging 0.97
R0746:Rtl1 UTSW 12 109,559,394 (GRCm39) missense probably damaging 1.00
R1353:Rtl1 UTSW 12 109,558,633 (GRCm39) missense probably benign 0.00
R1868:Rtl1 UTSW 12 109,556,970 (GRCm39) missense probably damaging 1.00
R1935:Rtl1 UTSW 12 109,558,354 (GRCm39) missense probably benign 0.42
R2000:Rtl1 UTSW 12 109,560,321 (GRCm39) missense probably damaging 1.00
R2094:Rtl1 UTSW 12 109,557,831 (GRCm39) missense unknown
R2125:Rtl1 UTSW 12 109,560,355 (GRCm39) missense possibly damaging 0.64
R2166:Rtl1 UTSW 12 109,556,988 (GRCm39) missense probably damaging 1.00
R2247:Rtl1 UTSW 12 109,561,413 (GRCm39) missense possibly damaging 0.77
R2274:Rtl1 UTSW 12 109,561,101 (GRCm39) missense unknown
R2919:Rtl1 UTSW 12 109,557,582 (GRCm39) missense unknown
R2998:Rtl1 UTSW 12 109,561,530 (GRCm39) missense probably damaging 0.99
R4554:Rtl1 UTSW 12 109,560,762 (GRCm39) missense possibly damaging 0.53
R4566:Rtl1 UTSW 12 109,559,293 (GRCm39) missense probably damaging 1.00
R4887:Rtl1 UTSW 12 109,558,138 (GRCm39) missense probably damaging 0.96
R5512:Rtl1 UTSW 12 109,557,805 (GRCm39) missense unknown
R5616:Rtl1 UTSW 12 109,559,173 (GRCm39) missense unknown
R5644:Rtl1 UTSW 12 109,558,013 (GRCm39) missense probably benign 0.03
R5647:Rtl1 UTSW 12 109,561,113 (GRCm39) missense unknown
R5695:Rtl1 UTSW 12 109,560,531 (GRCm39) missense probably damaging 1.00
R5714:Rtl1 UTSW 12 109,560,114 (GRCm39) missense probably damaging 0.99
R5786:Rtl1 UTSW 12 109,559,053 (GRCm39) missense possibly damaging 0.89
R5917:Rtl1 UTSW 12 109,558,087 (GRCm39) missense possibly damaging 0.82
R5948:Rtl1 UTSW 12 109,557,033 (GRCm39) missense possibly damaging 0.86
R6051:Rtl1 UTSW 12 109,559,458 (GRCm39) missense probably damaging 1.00
R6251:Rtl1 UTSW 12 109,560,083 (GRCm39) missense probably benign 0.16
R6342:Rtl1 UTSW 12 109,558,735 (GRCm39) missense possibly damaging 0.50
R6433:Rtl1 UTSW 12 109,561,630 (GRCm39) missense unknown
R6815:Rtl1 UTSW 12 109,560,937 (GRCm39) missense probably damaging 0.98
R6968:Rtl1 UTSW 12 109,561,113 (GRCm39) missense unknown
R7002:Rtl1 UTSW 12 109,560,381 (GRCm39) missense probably damaging 0.97
R7020:Rtl1 UTSW 12 109,558,749 (GRCm39) missense possibly damaging 0.72
R7026:Rtl1 UTSW 12 109,559,595 (GRCm39) missense probably damaging 0.99
R7027:Rtl1 UTSW 12 109,557,848 (GRCm39) small deletion probably benign
R7196:Rtl1 UTSW 12 109,559,221 (GRCm39) missense possibly damaging 0.83
R7239:Rtl1 UTSW 12 109,558,909 (GRCm39) missense probably benign 0.05
R7312:Rtl1 UTSW 12 109,561,672 (GRCm39) missense unknown
R7476:Rtl1 UTSW 12 109,557,539 (GRCm39) missense unknown
R7589:Rtl1 UTSW 12 109,560,279 (GRCm39) missense possibly damaging 0.91
R7655:Rtl1 UTSW 12 109,557,442 (GRCm39) missense unknown
R7656:Rtl1 UTSW 12 109,557,442 (GRCm39) missense unknown
R7657:Rtl1 UTSW 12 109,561,818 (GRCm39) missense possibly damaging 0.94
R7720:Rtl1 UTSW 12 109,560,864 (GRCm39) missense possibly damaging 0.96
R7772:Rtl1 UTSW 12 109,559,619 (GRCm39) missense probably damaging 1.00
R7840:Rtl1 UTSW 12 109,560,589 (GRCm39) missense probably benign 0.08
R7890:Rtl1 UTSW 12 109,559,251 (GRCm39) missense possibly damaging 0.57
R7893:Rtl1 UTSW 12 109,560,355 (GRCm39) missense possibly damaging 0.64
R7894:Rtl1 UTSW 12 109,561,031 (GRCm39) missense possibly damaging 0.70
R7909:Rtl1 UTSW 12 109,558,914 (GRCm39) missense possibly damaging 0.95
R7909:Rtl1 UTSW 12 109,556,611 (GRCm39) missense unknown
R7986:Rtl1 UTSW 12 109,558,492 (GRCm39) missense possibly damaging 0.95
R8007:Rtl1 UTSW 12 109,558,060 (GRCm39) missense possibly damaging 0.86
R8146:Rtl1 UTSW 12 109,557,145 (GRCm39) missense probably benign 0.01
R8193:Rtl1 UTSW 12 109,558,650 (GRCm39) missense probably benign 0.03
R8263:Rtl1 UTSW 12 109,560,180 (GRCm39) missense probably damaging 0.99
R8273:Rtl1 UTSW 12 109,559,149 (GRCm39) missense possibly damaging 0.92
R8512:Rtl1 UTSW 12 109,561,051 (GRCm39) missense unknown
R8514:Rtl1 UTSW 12 109,560,307 (GRCm39) missense possibly damaging 0.52
R8748:Rtl1 UTSW 12 109,561,492 (GRCm39) missense probably benign 0.39
R9036:Rtl1 UTSW 12 109,559,691 (GRCm39) missense probably benign 0.03
R9104:Rtl1 UTSW 12 109,560,718 (GRCm39) missense probably benign 0.21
R9151:Rtl1 UTSW 12 109,560,007 (GRCm39) missense
R9238:Rtl1 UTSW 12 109,561,017 (GRCm39) missense possibly damaging 0.72
R9292:Rtl1 UTSW 12 109,556,673 (GRCm39) missense possibly damaging 0.91
R9329:Rtl1 UTSW 12 109,556,673 (GRCm39) missense possibly damaging 0.91
R9332:Rtl1 UTSW 12 109,557,291 (GRCm39) missense probably benign 0.01
R9342:Rtl1 UTSW 12 109,558,884 (GRCm39) missense probably damaging 1.00
R9350:Rtl1 UTSW 12 109,557,226 (GRCm39) nonsense probably null
R9446:Rtl1 UTSW 12 109,556,604 (GRCm39) makesense probably null
R9523:Rtl1 UTSW 12 109,561,113 (GRCm39) missense unknown
R9524:Rtl1 UTSW 12 109,556,973 (GRCm39) missense probably damaging 1.00
R9535:Rtl1 UTSW 12 109,561,698 (GRCm39) missense unknown
R9535:Rtl1 UTSW 12 109,557,171 (GRCm39) missense probably damaging 1.00
R9564:Rtl1 UTSW 12 109,556,713 (GRCm39) missense probably benign 0.19
R9615:Rtl1 UTSW 12 109,556,835 (GRCm39) missense possibly damaging 0.65
R9661:Rtl1 UTSW 12 109,557,346 (GRCm39) missense possibly damaging 0.79
R9674:Rtl1 UTSW 12 109,559,024 (GRCm39) missense possibly damaging 0.50
R9720:Rtl1 UTSW 12 109,559,882 (GRCm39) missense possibly damaging 0.50
Z1088:Rtl1 UTSW 12 109,558,753 (GRCm39) missense probably benign 0.02
Predicted Primers PCR Primer
(F):5'- TGTGCTGGATCTGAGCGAAG -3'
(R):5'- AGACGACCTGCAACGTTAC -3'

Sequencing Primer
(F):5'- AGCTGGCCGAGGCACAAG -3'
(R):5'- ACGTTACCGTCAGTGTGGC -3'
Posted On 2016-09-06