Incidental Mutation 'R7657:Rtl1'
ID 591293
Institutional Source Beutler Lab
Gene Symbol Rtl1
Ensembl Gene ENSMUSG00000085925
Gene Name retrotransposon Gaglike 1
Synonyms Mart1, Mar, Mor1
MMRRC Submission 045733-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7657 (G1)
Quality Score 225.009
Status Validated
Chromosome 12
Chromosomal Location 109555627-109566764 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 109561818 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 7 (D7G)
Ref Sequence ENSEMBL: ENSMUSP00000115957 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000149046]
AlphaFold Q7M732
Predicted Effect possibly damaging
Transcript: ENSMUST00000149046
AA Change: D7G

PolyPhen 2 Score 0.942 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000115957
Gene: ENSMUSG00000085925
AA Change: D7G

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
Meta Mutation Damage Score 0.0877 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency 100% (80/80)
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: 80 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310033P09Rik A G 11: 59,099,337 (GRCm39) E28G possibly damaging Het
Acot6 G A 12: 84,153,304 (GRCm39) G182D possibly damaging Het
Actl9 A G 17: 33,652,014 (GRCm39) T25A probably benign Het
Adam26b G A 8: 43,974,579 (GRCm39) T141I possibly damaging Het
Agl T C 3: 116,572,812 (GRCm39) H148R Het
Angptl1 A G 1: 156,684,790 (GRCm39) I320V probably benign Het
Arhgef10 C T 8: 15,029,893 (GRCm39) R932C probably damaging Het
Atp13a2 A G 4: 140,719,815 (GRCm39) E91G possibly damaging Het
Bptf T A 11: 106,965,555 (GRCm39) E1213V probably damaging Het
C530025M09Rik A G 2: 149,672,541 (GRCm39) V198A unknown Het
Casd1 A T 6: 4,619,773 (GRCm39) I173F probably benign Het
Ccng2 C G 5: 93,421,202 (GRCm39) S237R probably benign Het
Col1a2 A T 6: 4,527,152 (GRCm39) K627M probably null Het
Ctcfl G A 2: 172,955,449 (GRCm39) T271I possibly damaging Het
Dctn2 T C 10: 127,102,383 (GRCm39) Y6H probably damaging Het
Denr T C 5: 124,046,263 (GRCm39) V31A probably damaging Het
Entpd7 T C 19: 43,713,906 (GRCm39) F422L possibly damaging Het
Fastkd5 G C 2: 130,458,176 (GRCm39) P138R probably benign Het
Fmn1 G T 2: 113,355,538 (GRCm39) A758S unknown Het
Fmo2 A G 1: 162,716,413 (GRCm39) V58A probably damaging Het
Fmo6 A G 1: 162,750,285 (GRCm39) I257T probably benign Het
Foxn1 T C 11: 78,256,790 (GRCm39) T302A probably benign Het
Ganab C T 19: 8,884,721 (GRCm39) L175F probably damaging Het
Gga1 A T 15: 78,773,327 (GRCm39) probably null Het
Gjd3 G T 11: 98,873,586 (GRCm39) S86* probably null Het
Gm1330 A G 2: 148,841,154 (GRCm39) probably null Het
Gm18596 A C 10: 77,577,947 (GRCm39) S176A unknown Het
Gnl2 A G 4: 124,923,951 (GRCm39) S10G probably benign Het
Gpsm2 G A 3: 108,608,061 (GRCm39) A239V probably damaging Het
Grik2 T C 10: 49,659,247 (GRCm39) R37G probably benign Het
Grm3 A G 5: 9,561,452 (GRCm39) probably null Het
Gtpbp3 T C 8: 71,943,765 (GRCm39) L216P probably benign Het
Hhla1 T C 15: 65,837,308 (GRCm39) T99A probably damaging Het
Igtp A T 11: 58,097,654 (GRCm39) Q275L probably benign Het
Itga6 G A 2: 71,676,595 (GRCm39) A993T probably benign Het
Jakmip3 T A 7: 138,620,903 (GRCm39) I234N probably damaging Het
Kcnh7 A G 2: 62,566,379 (GRCm39) F851L probably damaging Het
Krr1 A G 10: 111,811,504 (GRCm39) Y66C probably damaging Het
Krt33a T A 11: 99,906,693 (GRCm39) Q94L probably benign Het
Mat1a A T 14: 40,844,476 (GRCm39) K369* probably null Het
Mbd1 T G 18: 74,407,804 (GRCm39) L277R probably damaging Het
Mmp21 C T 7: 133,280,562 (GRCm39) G136D probably benign Het
Mroh3 A G 1: 136,109,532 (GRCm39) Y892H possibly damaging Het
Ncbp3 G A 11: 72,964,193 (GRCm39) R381Q probably damaging Het
Nlrp2 T A 7: 5,322,167 (GRCm39) I827L probably benign Het
Nrip1 T A 16: 76,091,587 (GRCm39) probably null Het
Or2ak4 A T 11: 58,648,755 (GRCm39) D88V probably benign Het
Or4f6 A G 2: 111,839,093 (GRCm39) V146A probably benign Het
Or5w13 C T 2: 87,523,336 (GRCm39) V297I probably damaging Het
Oxt C T 2: 130,418,710 (GRCm39) P107L possibly damaging Het
Pcdhga2 G A 18: 37,803,481 (GRCm39) V442M probably damaging Het
Phtf1 T G 3: 103,876,429 (GRCm39) S10A probably benign Het
Plb1 A C 5: 32,487,211 (GRCm39) N902T probably damaging Het
Plppr3 T C 10: 79,702,272 (GRCm39) I267V probably benign Het
Pms2 C A 5: 143,856,357 (GRCm39) H278Q possibly damaging Het
Pmvk T A 3: 89,376,158 (GRCm39) S154T possibly damaging Het
Polr3b T A 10: 84,491,855 (GRCm39) M338K probably damaging Het
Ppp1r21 T A 17: 88,863,110 (GRCm39) I283N probably damaging Het
Ptprj A T 2: 90,282,501 (GRCm39) probably null Het
Rft1 T A 14: 30,388,724 (GRCm39) L216H probably damaging Het
Rpl3 G A 15: 79,965,258 (GRCm39) P174S probably benign Het
Slc13a2 A G 11: 78,289,223 (GRCm39) V496A probably damaging Het
Slc14a1 A G 18: 78,156,879 (GRCm39) probably null Het
Slc8a3 T C 12: 81,361,158 (GRCm39) R554G probably damaging Het
Spata31d1b T C 13: 59,863,577 (GRCm39) S242P possibly damaging Het
Spocd1 G A 4: 129,823,535 (GRCm39) V111I Het
Stxbp5l G A 16: 37,030,534 (GRCm39) A479V probably null Het
Tasor2 A G 13: 3,623,777 (GRCm39) S2058P probably damaging Het
Tmem238 C G 7: 4,792,226 (GRCm39) G106R probably damaging Het
Trak1 T G 9: 121,301,652 (GRCm39) Y803D probably damaging Het
Trim5 T C 7: 103,925,884 (GRCm39) S226G possibly damaging Het
Trim6 T A 7: 103,881,068 (GRCm39) D282E possibly damaging Het
Ube2e2 A G 14: 18,586,997 (GRCm38) V121A probably benign Het
Ufd1 T G 16: 18,636,713 (GRCm39) M77R probably benign Het
Unc13c C T 9: 73,441,185 (GRCm39) probably null Het
Wfs1 A G 5: 37,125,578 (GRCm39) S438P probably benign Het
Zbtb6 A C 2: 37,319,087 (GRCm39) D280E probably benign Het
Zfp595 G A 13: 67,465,817 (GRCm39) L152F probably damaging Het
Zfpm2 A G 15: 40,966,671 (GRCm39) E1052G possibly damaging Het
Zmym5 A G 14: 57,041,653 (GRCm39) V150A probably benign 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
R5399:Rtl1 UTSW 12 109,556,736 (GRCm39) missense probably damaging 1.00
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
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'- GCTCTTGCATTTCCTTGAGG -3'
(R):5'- GACCCTGCCATCTTGAGAAC -3'

Sequencing Primer
(F):5'- ATTTCCTTGAGGGGGCCAC -3'
(R):5'- CCTGCCATCTTGAGAACCTAAATTG -3'
Posted On 2019-11-12