Mutagenetix > Incidental Mutation

Incidental Mutation 'R4708:Rlig1'

355430

Institutional Source

Beutler Lab

Gene Symbol

Rlig1

Ensembl Gene

ENSMUSG00000046567

Gene Name

RNA 5'-phosphate and 3'-OH ligase 1

Synonyms

4930430F08Rik

MMRRC Submission

042017-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.167) question?

Stock #

R4708 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

100408136-100425252 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 100414243 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 139 (I139V)

Ref Sequence

ENSEMBL: ENSMUSP00000152035 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000054471] [ENSMUST00000164751] [ENSMUST00000218821] [ENSMUST00000219765] [ENSMUST00000220346]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000054471
AA Change: I119V

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)

Predicted Effect

probably benign
Transcript: ENSMUST00000164751

SMART Domains

Protein: ENSMUSP00000130899
Gene: ENSMUSG00000019971

Domain	Start	End	E-Value	Type
coiled coil region	59	298	N/A	INTRINSIC
coiled coil region	319	566	N/A	INTRINSIC
coiled coil region	598	662	N/A	INTRINSIC
coiled coil region	697	754	N/A	INTRINSIC
coiled coil region	780	875	N/A	INTRINSIC
internal_repeat_2	884	894	1.1e-5	PROSPERO
coiled coil region	986	1028	N/A	INTRINSIC
internal_repeat_2	1057	1067	1.1e-5	PROSPERO
coiled coil region	1071	1109	N/A	INTRINSIC
low complexity region	1140	1156	N/A	INTRINSIC
internal_repeat_1	1176	1206	8.72e-8	PROSPERO
coiled coil region	1221	1250	N/A	INTRINSIC
Pfam:CEP209_CC5	1290	1417	3.8e-55	PFAM
low complexity region	1476	1493	N/A	INTRINSIC
internal_repeat_1	1498	1525	8.72e-8	PROSPERO
coiled coil region	1535	1595	N/A	INTRINSIC
coiled coil region	1624	1716	N/A	INTRINSIC
coiled coil region	1776	2328	N/A	INTRINSIC
low complexity region	2333	2347	N/A	INTRINSIC
coiled coil region	2377	2453	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000218156

Predicted Effect

probably benign
Transcript: ENSMUST00000218328

Predicted Effect

probably benign
Transcript: ENSMUST00000218821
AA Change: I139V

PolyPhen 2 Score 0.074 (Sensitivity: 0.93; Specificity: 0.85)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000219410

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000219643

Predicted Effect

probably benign
Transcript: ENSMUST00000219765

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000219698

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000219889

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000219995

Predicted Effect

probably benign
Transcript: ENSMUST00000220346

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000219790

Meta Mutation Damage Score

0.0736

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.8%

Validation Efficiency

97% (68/70)

Allele List at MGI

Other mutations in this stock

Total: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610021A01Rik	G	A	7: 41,261,309 (GRCm39)	G2D	probably damaging	Het
4930505A04Rik	T	C	11: 30,404,717 (GRCm39)	Y62C	probably damaging	Het
Aadacl4	A	C	4: 144,349,899 (GRCm39)	K385N	probably benign	Het
Abcb4	A	T	5: 8,965,125 (GRCm39)	T332S	possibly damaging	Het
Aco2	G	A	15: 81,794,117 (GRCm39)		probably null	Het
Aplf	G	T	6: 87,640,739 (GRCm39)	S69Y	probably damaging	Het
Arhgap27	A	G	11: 103,224,388 (GRCm39)		probably benign	Het
B4galnt1	T	A	10: 127,005,684 (GRCm39)	Y262N	probably damaging	Het
Bag4	C	T	8: 26,259,516 (GRCm39)	A228T	probably benign	Het
Ccdc62	T	G	5: 124,068,925 (GRCm39)		probably null	Het
Cd109	T	A	9: 78,579,871 (GRCm39)	I649K	probably benign	Het
Cd209b	T	C	8: 3,974,215 (GRCm39)	E99G	probably damaging	Het
Cep290	A	G	10: 100,359,126 (GRCm39)	K952R	probably benign	Het
Ces2a	A	G	8: 105,463,938 (GRCm39)	H190R	probably benign	Het
Clec14a	A	G	12: 58,314,489 (GRCm39)	S378P	probably benign	Het
Col27a1	A	G	4: 63,202,150 (GRCm39)	Q947R	probably benign	Het
Dennd3	A	G	15: 73,395,344 (GRCm39)	T146A	probably damaging	Het
Dpy19l4	T	A	4: 11,277,970 (GRCm39)	M486L	probably benign	Het
Dysf	C	A	6: 84,074,697 (GRCm39)	D499E	probably damaging	Het
Eif4enif1	T	G	11: 3,170,323 (GRCm39)	H125Q	probably damaging	Het
Fcgbp	A	T	7: 27,794,386 (GRCm39)	M1197L	probably benign	Het
Fubp3	C	T	2: 31,498,122 (GRCm39)	T92I	probably benign	Het
Gm19426	T	C	2: 84,573,803 (GRCm39)		probably null	Het
Gtf2ird2	A	G	5: 134,245,140 (GRCm39)	H466R	probably damaging	Het
Hdac5	T	C	11: 102,093,019 (GRCm39)	S573G	probably damaging	Het
Iars2	A	T	1: 185,021,554 (GRCm39)	M916K	probably benign	Het
Insr	A	T	8: 3,261,346 (GRCm39)		probably benign	Het
Itgam	T	C	7: 127,700,709 (GRCm39)	V493A	probably damaging	Het
Ivl	T	A	3: 92,479,057 (GRCm39)	K336I	probably damaging	Het
Kcng2	A	G	18: 80,366,067 (GRCm39)	I95T	probably damaging	Het
Lap3	A	G	5: 45,668,480 (GRCm39)	R431G	probably damaging	Het
Lrrc66	T	C	5: 73,787,005 (GRCm39)	H115R	probably benign	Het
Morc3	T	C	16: 93,670,126 (GRCm39)	V767A	probably benign	Het
Mttp	A	G	3: 137,839,859 (GRCm39)		probably benign	Het
Myo1c	C	T	11: 75,560,856 (GRCm39)	R770*	probably null	Het
Nat9	G	A	11: 115,074,269 (GRCm39)	T133M	probably damaging	Het
Nectin4	T	C	1: 171,212,714 (GRCm39)	I349T	probably benign	Het
Nlrp4a	A	G	7: 26,163,533 (GRCm39)	E900G	probably benign	Het
Nlrp9c	A	T	7: 26,084,265 (GRCm39)	M438K	probably benign	Het
Or2y14	T	A	11: 49,405,216 (GRCm39)	Y250*	probably null	Het
Or52p2	A	T	7: 102,237,043 (GRCm39)	D302E	probably benign	Het
Or5b21	A	T	19: 12,839,261 (GRCm39)	I41F	probably benign	Het
Parp6	T	C	9: 59,549,052 (GRCm39)	I507T	probably damaging	Het
Pde6c	G	A	19: 38,169,341 (GRCm39)	E804K	possibly damaging	Het
Plscr2	A	G	9: 92,173,067 (GRCm39)	Y203C	probably damaging	Het
Ptprs	A	G	17: 56,735,067 (GRCm39)	W216R	probably damaging	Het
Rhof	T	A	5: 123,258,454 (GRCm39)	T126S	probably benign	Het
Riox2	A	G	16: 59,296,045 (GRCm39)	I49V	probably benign	Het
Rusf1	A	G	7: 127,873,852 (GRCm39)	V345A	probably benign	Het
Shld2	A	G	14: 33,989,790 (GRCm39)	V372A	probably benign	Het
Spata31e2	A	T	1: 26,723,521 (GRCm39)	V553D	possibly damaging	Het
Tmc6	A	T	11: 117,659,774 (GRCm39)	C750S	probably benign	Het
Tmem231	C	A	8: 112,660,418 (GRCm39)		probably benign	Het
Tmem94	T	A	11: 115,677,121 (GRCm39)	I131N	possibly damaging	Het
Tmx3	T	C	18: 90,539,163 (GRCm39)		probably null	Het
Tnfrsf21	C	T	17: 43,349,123 (GRCm39)	T245I	possibly damaging	Het
Ttbk2	C	A	2: 120,570,342 (GRCm39)	R1201S	probably damaging	Het
Vmn2r102	A	T	17: 19,914,576 (GRCm39)	M714L	probably benign	Het
Vmn2r109	A	G	17: 20,761,605 (GRCm39)	L584S	probably damaging	Het
Vmn2r53	T	A	7: 12,335,129 (GRCm39)	H177L	probably benign	Het
Vnn1	T	A	10: 23,773,250 (GRCm39)	D92E	probably benign	Het
Zan	T	C	5: 137,444,974 (GRCm39)	I1762V	unknown	Het
Zbtb20	G	T	16: 43,431,039 (GRCm39)	A517S	probably damaging	Het
Zfhx4	A	G	3: 5,310,563 (GRCm39)		probably null	Het
Zfp560	T	C	9: 20,263,214 (GRCm39)	E54G	possibly damaging	Het
Zfp719	C	T	7: 43,239,656 (GRCm39)	H415Y	probably damaging	Het
Zmynd11	A	C	13: 9,745,789 (GRCm39)	V188G	probably damaging	Het

Other mutations in Rlig1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01314:Rlig1	APN	10	100,409,473 (GRCm39)	missense	probably damaging	0.97
IGL01775:Rlig1	APN	10	100,419,799 (GRCm39)	missense	probably benign	0.41
PIT4495001:Rlig1	UTSW	10	100,419,812 (GRCm39)	missense	probably damaging	1.00
R0206:Rlig1	UTSW	10	100,422,056 (GRCm39)	nonsense	probably null
R0731:Rlig1	UTSW	10	100,422,065 (GRCm39)	missense	probably damaging	1.00
R1955:Rlig1	UTSW	10	100,413,166 (GRCm39)	missense	probably damaging	1.00
R2011:Rlig1	UTSW	10	100,419,820 (GRCm39)	missense	probably damaging	0.99
R4680:Rlig1	UTSW	10	100,414,243 (GRCm39)	missense	probably benign	0.07
R4682:Rlig1	UTSW	10	100,414,243 (GRCm39)	missense	probably benign	0.07
R4683:Rlig1	UTSW	10	100,414,243 (GRCm39)	missense	probably benign	0.07
R4709:Rlig1	UTSW	10	100,414,243 (GRCm39)	missense	probably benign	0.07
R4742:Rlig1	UTSW	10	100,414,243 (GRCm39)	missense	probably benign	0.07
R4743:Rlig1	UTSW	10	100,414,243 (GRCm39)	missense	probably benign	0.07
R6716:Rlig1	UTSW	10	100,409,478 (GRCm39)	missense	probably benign	0.00
R7185:Rlig1	UTSW	10	100,425,073 (GRCm39)	start gained	probably benign
R8103:Rlig1	UTSW	10	100,413,110 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- ACAAGTCGCTCTAAGCAATATCTG -3'
(R):5'- AGACGGTAGTGTGCAACGTG -3'

Sequencing Primer
(F):5'- GTCGCTCTAAGCAATATCTGATAAAG -3'
(R):5'- CAACGTGGTAGTGTACTAAAAGTTGC -3'

Posted On

2015-10-21