Mutagenetix > Incidental Mutation

Incidental Mutation 'R7986:Rtl1'

651498

Institutional Source

Beutler Lab

Gene Symbol

Rtl1

Ensembl Gene

ENSMUSG00000085925

Gene Name

retrotransposon Gaglike 1

Synonyms

Mart1, Mar, Mor1

MMRRC Submission

046027-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7986 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

109555627-109566764 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 109558492 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 1116 (S1116P)

Ref Sequence

ENSEMBL: ENSMUSP00000115957 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000149046]

AlphaFold

Q7M732

Predicted Effect

possibly damaging
Transcript: ENSMUST00000149046
AA Change: S1116P

PolyPhen 2 Score 0.952 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000115957
Gene: ENSMUSG00000085925
AA Change: S1116P

Domain	Start	End	E-Value	Type
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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

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: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts1	G	T	16: 85,596,435 (GRCm39)	A401D	probably damaging	Het
Akap10	C	T	11: 61,820,890 (GRCm39)	G5R	probably damaging	Het
Arhgap21	A	C	2: 20,867,967 (GRCm39)	L1023W	probably damaging	Het
Bpifb4	A	G	2: 153,799,650 (GRCm39)	N339S	probably benign	Het
Btbd17	A	G	11: 114,683,341 (GRCm39)	Y124H	probably damaging	Het
Cacna1a	C	G	8: 85,365,408 (GRCm39)	R2184G	probably benign	Het
Cavin1	A	G	11: 100,861,102 (GRCm39)	I64T	probably damaging	Het
Cby3	A	G	11: 50,250,106 (GRCm39)	H9R	possibly damaging	Het
Ccdc141	A	G	2: 76,845,461 (GRCm39)	L1202P	probably benign	Het
Cd109	A	G	9: 78,596,048 (GRCm39)	I794V	possibly damaging	Het
Col12a1	C	T	9: 79,511,674 (GRCm39)		probably null	Het
Col6a2	A	G	10: 76,450,972 (GRCm39)	L23P	probably benign	Het
Csf1r	A	G	18: 61,247,904 (GRCm39)	H324R	probably benign	Het
D430041D05Rik	A	G	2: 104,087,096 (GRCm39)	S627P	probably damaging	Het
Dffb	G	A	4: 154,054,504 (GRCm39)	S195F	probably damaging	Het
Fstl5	T	A	3: 76,337,097 (GRCm39)	Y219N	probably damaging	Het
Gm29106	A	T	1: 118,128,000 (GRCm39)	H564L	possibly damaging	Het
Gpt2	T	A	8: 86,235,839 (GRCm39)	C158*	probably null	Het
Grin1	G	T	2: 25,185,841 (GRCm39)	A872D	probably damaging	Het
Hoxa1	T	C	6: 52,135,018 (GRCm39)	S62G	probably benign	Het
Krt28	T	C	11: 99,257,651 (GRCm39)	N397D	probably benign	Het
Ldlrad4	G	T	18: 68,368,740 (GRCm39)	A66S	possibly damaging	Het
Llgl1	G	T	11: 60,602,221 (GRCm39)	A755S	probably benign	Het
Lmod2	A	G	6: 24,603,448 (GRCm39)	E141G	possibly damaging	Het
Loxhd1	A	T	18: 77,462,890 (GRCm39)	T910S	possibly damaging	Het
Masp2	A	G	4: 148,687,283 (GRCm39)	Y55C	probably damaging	Het
Nek10	A	C	14: 15,001,020 (GRCm38)	S1067R	probably benign	Het
Nemp2	C	T	1: 52,669,981 (GRCm39)	A22V	probably benign	Het
Npy2r	T	A	3: 82,448,803 (GRCm39)		probably null	Het
Nr1h4	A	T	10: 89,290,634 (GRCm39)	S469T	possibly damaging	Het
Nr4a3	T	C	4: 48,055,954 (GRCm39)	Y327H	probably damaging	Het
Or10ag52	A	G	2: 87,043,922 (GRCm39)	I229V	probably benign	Het
Or5an1b	C	T	19: 12,300,102 (GRCm39)	V30I	probably benign	Het
Pramel26	A	T	4: 143,538,590 (GRCm39)	L127*	probably null	Het
Prss1l	T	C	6: 41,373,058 (GRCm39)	I110T	probably damaging	Het
Ptpdc1	G	A	13: 48,746,046 (GRCm39)	A118V	probably damaging	Het
Raph1	T	C	1: 60,535,445 (GRCm39)	Y73C		Het
Secisbp2	T	C	13: 51,819,395 (GRCm39)	I325T	probably damaging	Het
Setd5	T	C	6: 113,105,418 (GRCm39)	S817P	probably benign	Het
Sirt6	A	G	10: 81,458,344 (GRCm39)	L303P	probably benign	Het
Slc46a2	G	T	4: 59,911,858 (GRCm39)	F451L	probably benign	Het
Sorbs1	T	A	19: 40,353,449 (GRCm39)	I219F	probably damaging	Het
Tmem178	A	G	17: 81,308,273 (GRCm39)	I223V	possibly damaging	Het
Trps1	T	G	15: 50,525,132 (GRCm39)	T933P	probably damaging	Het
Trps1	A	G	15: 50,753,019 (GRCm39)	F16S	probably benign	Het
Virma	T	A	4: 11,540,023 (GRCm39)	S1447R	probably benign	Het
Vmn1r230	T	C	17: 21,067,119 (GRCm39)	Y103H	probably damaging	Het
Wdfy4	G	A	14: 32,826,072 (GRCm39)	P1193L		Het
Ybx3	T	A	6: 131,356,362 (GRCm39)	R170*	probably null	Het
Zfp423	T	C	8: 88,506,978 (GRCm39)	D1122G	probably benign	Het

Other mutations in Rtl1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
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'- AGGATCCTCATCTCCACTCG -3'
(R):5'- ACCTTATGAACCTCATCGTGGG -3'

Sequencing Primer
(F):5'- GTACTCCACCTCCATTGTAGAGAGG -3'
(R):5'- TCATCGTGGGGTGCCCTG -3'

Posted On

2020-09-15