Mutagenetix > Incidental Mutation

Incidental Mutation 'R4065:Ltn1'

316088

Institutional Source

Beutler Lab

Gene Symbol

Ltn1

Ensembl Gene

ENSMUSG00000052299

Gene Name

listerin E3 ubiquitin protein ligase 1

Synonyms

Listerin, Zfp294, Rnf160, 4930528H02Rik

MMRRC Submission

040972-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4065 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

87173539-87229500 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 87213118 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 481 (Y481C)

Ref Sequence

ENSEMBL: ENSMUSP00000156299 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000039449] [ENSMUST00000232095]

AlphaFold

Q6A009

Predicted Effect

possibly damaging
Transcript: ENSMUST00000039449
AA Change: Y481C

PolyPhen 2 Score 0.627 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000038775
Gene: ENSMUSG00000052299
AA Change: Y481C

Domain	Start	End	E-Value	Type
low complexity region	160	176	N/A	INTRINSIC
low complexity region	400	410	N/A	INTRINSIC
low complexity region	509	522	N/A	INTRINSIC
low complexity region	553	569	N/A	INTRINSIC
low complexity region	815	832	N/A	INTRINSIC
low complexity region	1380	1392	N/A	INTRINSIC
low complexity region	1427	1451	N/A	INTRINSIC
RING	1716	1762	1.05e-1	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000083713

Predicted Effect

possibly damaging
Transcript: ENSMUST00000232095
AA Change: Y481C

PolyPhen 2 Score 0.838 (Sensitivity: 0.84; Specificity: 0.93)

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.2%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Like most RING finger proteins, LTN1 functions as an E3 ubiquitin ligase (Chu et al., 2009 [PubMed 19196968]).[supplied by OMIM, Nov 2010]
PHENOTYPE: Mice homozygous for a gene trap allele display embryonic lethality. Mice homozygous for a point mutation display progressive neuron degeneration and age dependent motor deficits. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 48 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933434E20Rik	C	T	3: 89,966,073 (GRCm39)	R178*	probably null	Het
Abcc9	T	C	6: 142,591,616 (GRCm39)	E769G	probably damaging	Het
Adcy9	C	A	16: 4,106,298 (GRCm39)	V939F	probably damaging	Het
Atg2a	T	C	19: 6,308,396 (GRCm39)	F1643S	probably damaging	Het
B430305J03Rik	A	G	3: 61,271,646 (GRCm39)		probably benign	Het
C2cd5	A	G	6: 143,019,397 (GRCm39)	I306T	probably benign	Het
Camk1d	A	T	2: 5,570,584 (GRCm39)	F26I	probably damaging	Het
Cant1	G	T	11: 118,298,823 (GRCm39)	D313E	probably benign	Het
Dhx29	T	A	13: 113,101,276 (GRCm39)		probably null	Het
Dnah12	A	G	14: 26,492,405 (GRCm39)	I1182V	probably benign	Het
Dnajc21	A	G	15: 10,451,639 (GRCm39)		probably null	Het
Dnajc7	T	C	11: 100,492,607 (GRCm39)	Y38C	probably benign	Het
Dpyd	AAT	AATGTATATATAT	3: 118,690,738 (GRCm39)		probably benign	Het
Dync2i2	A	G	2: 29,922,820 (GRCm39)	L309P	probably benign	Het
Fat4	A	T	3: 39,063,346 (GRCm39)	H4434L	probably benign	Het
Fbxo16	T	A	14: 65,508,278 (GRCm39)	N31K	probably damaging	Het
Foxj3	T	C	4: 119,467,206 (GRCm39)	I183T	probably benign	Het
Fras1	T	A	5: 96,918,542 (GRCm39)	I3526K	possibly damaging	Het
Fshr	T	C	17: 89,293,394 (GRCm39)	Y428C	probably damaging	Het
Gm11437	A	G	11: 84,055,337 (GRCm39)	V93A	probably benign	Het
Gm12258	C	T	11: 58,749,352 (GRCm39)	L176F	probably benign	Het
Grem1	A	G	2: 113,580,033 (GRCm39)	L156P	probably damaging	Het
Hecw1	T	C	13: 14,491,016 (GRCm39)	S659G	probably damaging	Het
Lamc3	C	A	2: 31,835,270 (GRCm39)	H1530Q	probably benign	Het
Man1c1	G	C	4: 134,430,749 (GRCm39)	P11R	probably damaging	Het
Mga	T	C	2: 119,777,483 (GRCm39)	V1846A	probably damaging	Het
Mthfd1l	A	G	10: 3,982,242 (GRCm39)	H483R	probably damaging	Het
Muc4	A	T	16: 32,569,869 (GRCm39)	I310F	possibly damaging	Het
Mvp	A	G	7: 126,595,489 (GRCm39)	V207A	probably damaging	Het
Nsun2	T	C	13: 69,760,579 (GRCm39)		probably null	Het
Or13a26	T	C	7: 140,284,182 (GRCm39)	L6P	probably benign	Het
Or8g55	T	C	9: 39,784,718 (GRCm39)	I49T	possibly damaging	Het
Pcnx4	T	C	12: 72,603,134 (GRCm39)		probably null	Het
Plxna4	T	A	6: 32,213,300 (GRCm39)	K637*	probably null	Het
Ppm1d	A	G	11: 85,236,678 (GRCm39)	T486A	probably benign	Het
Prb1a	T	A	6: 132,184,658 (GRCm39)	Q325L	unknown	Het
Sf3a1	T	A	11: 4,117,824 (GRCm39)	F195L	probably damaging	Het
Spcs2	A	G	7: 99,494,012 (GRCm39)	I164T	possibly damaging	Het
Ssbp4	T	C	8: 71,052,210 (GRCm39)	T77A	possibly damaging	Het
Trpc5	T	A	X: 143,202,594 (GRCm39)	R545*	probably null	Het
Ugcg	C	T	4: 59,207,798 (GRCm39)	P46S	probably benign	Het
Uhrf1	T	A	17: 56,625,020 (GRCm39)	I521N	probably damaging	Het
Uros	A	G	7: 133,304,057 (GRCm39)		probably null	Het
Usp47	A	G	7: 111,652,623 (GRCm39)	D100G	probably benign	Het
Utp6	T	C	11: 79,837,073 (GRCm39)	R337G	probably damaging	Het
Vcan	T	C	13: 89,828,006 (GRCm39)	T3147A	probably damaging	Het
Wdfy3	C	T	5: 102,070,313 (GRCm39)	V1152I	probably benign	Het
Zfp654	G	A	16: 64,606,288 (GRCm39)	T638M	possibly damaging	Het

Other mutations in Ltn1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00328:Ltn1	APN	16	87,215,378 (GRCm39)	missense	probably benign	0.03
IGL01139:Ltn1	APN	16	87,212,897 (GRCm39)	missense	probably benign	0.04
IGL01359:Ltn1	APN	16	87,202,581 (GRCm39)	splice site	probably benign
IGL01503:Ltn1	APN	16	87,217,695 (GRCm39)	critical splice donor site	probably benign
IGL01529:Ltn1	APN	16	87,178,359 (GRCm39)	missense	probably benign	0.00
IGL02437:Ltn1	APN	16	87,194,889 (GRCm39)	missense	probably benign	0.04
IGL02658:Ltn1	APN	16	87,212,662 (GRCm39)	missense	probably damaging	1.00
IGL02890:Ltn1	APN	16	87,206,185 (GRCm39)	splice site	probably null
IGL02899:Ltn1	APN	16	87,179,547 (GRCm39)	missense	probably benign	0.34
IGL02902:Ltn1	APN	16	87,176,693 (GRCm39)	missense	possibly damaging	0.70
IGL03128:Ltn1	APN	16	87,212,832 (GRCm39)	missense	probably benign	0.00
IGL03392:Ltn1	APN	16	87,222,499 (GRCm39)	missense	probably damaging	1.00
IGL03046:Ltn1	UTSW	16	87,202,509 (GRCm39)	missense	probably benign	0.10
PIT4305001:Ltn1	UTSW	16	87,217,211 (GRCm39)	missense	probably damaging	1.00
PIT4366001:Ltn1	UTSW	16	87,177,728 (GRCm39)	nonsense	probably null
R0126:Ltn1	UTSW	16	87,222,528 (GRCm39)	missense	probably benign	0.00
R0164:Ltn1	UTSW	16	87,202,407 (GRCm39)	splice site	probably benign
R0165:Ltn1	UTSW	16	87,202,407 (GRCm39)	splice site	probably benign
R0280:Ltn1	UTSW	16	87,194,726 (GRCm39)	missense	probably damaging	1.00
R0565:Ltn1	UTSW	16	87,212,898 (GRCm39)	missense	probably benign	0.01
R0733:Ltn1	UTSW	16	87,209,395 (GRCm39)	missense	probably benign	0.01
R1034:Ltn1	UTSW	16	87,194,025 (GRCm39)	splice site	probably null
R1252:Ltn1	UTSW	16	87,212,918 (GRCm39)	missense	probably benign	0.00
R1524:Ltn1	UTSW	16	87,178,444 (GRCm39)	missense	probably damaging	1.00
R1746:Ltn1	UTSW	16	87,208,669 (GRCm39)	missense	possibly damaging	0.86
R1826:Ltn1	UTSW	16	87,212,504 (GRCm39)	missense	probably damaging	1.00
R1831:Ltn1	UTSW	16	87,197,034 (GRCm39)	missense	possibly damaging	0.94
R1839:Ltn1	UTSW	16	87,213,152 (GRCm39)	nonsense	probably null
R1860:Ltn1	UTSW	16	87,213,231 (GRCm39)	missense	probably benign	0.06
R1997:Ltn1	UTSW	16	87,178,525 (GRCm39)	missense	probably damaging	1.00
R2109:Ltn1	UTSW	16	87,212,530 (GRCm39)	missense	probably benign	0.03
R2134:Ltn1	UTSW	16	87,179,601 (GRCm39)	missense	probably damaging	1.00
R2135:Ltn1	UTSW	16	87,179,601 (GRCm39)	missense	probably damaging	1.00
R2193:Ltn1	UTSW	16	87,224,535 (GRCm39)	missense	probably damaging	1.00
R2307:Ltn1	UTSW	16	87,229,312 (GRCm39)	critical splice donor site	probably null
R2376:Ltn1	UTSW	16	87,217,695 (GRCm39)	critical splice donor site	probably null
R3054:Ltn1	UTSW	16	87,200,961 (GRCm39)	missense	probably benign	0.32
R3404:Ltn1	UTSW	16	87,213,103 (GRCm39)	missense	probably damaging	0.98
R3405:Ltn1	UTSW	16	87,213,103 (GRCm39)	missense	probably damaging	0.98
R3618:Ltn1	UTSW	16	87,217,787 (GRCm39)	missense	probably damaging	1.00
R4066:Ltn1	UTSW	16	87,213,118 (GRCm39)	missense	possibly damaging	0.84
R4067:Ltn1	UTSW	16	87,213,118 (GRCm39)	missense	possibly damaging	0.84
R4288:Ltn1	UTSW	16	87,194,876 (GRCm39)	missense	possibly damaging	0.57
R4436:Ltn1	UTSW	16	87,202,502 (GRCm39)	missense	probably benign	0.17
R4535:Ltn1	UTSW	16	87,223,174 (GRCm39)	missense	probably damaging	1.00
R4581:Ltn1	UTSW	16	87,198,912 (GRCm39)	critical splice donor site	probably null
R4669:Ltn1	UTSW	16	87,215,375 (GRCm39)	missense	possibly damaging	0.90
R4715:Ltn1	UTSW	16	87,215,382 (GRCm39)	missense	probably damaging	0.98
R4830:Ltn1	UTSW	16	87,176,582 (GRCm39)	missense	probably damaging	1.00
R4887:Ltn1	UTSW	16	87,195,697 (GRCm39)	nonsense	probably null
R4961:Ltn1	UTSW	16	87,194,679 (GRCm39)	missense	probably benign
R4992:Ltn1	UTSW	16	87,202,475 (GRCm39)	missense	possibly damaging	0.70
R5073:Ltn1	UTSW	16	87,224,628 (GRCm39)	missense	probably damaging	0.99
R5288:Ltn1	UTSW	16	87,212,899 (GRCm39)	missense	possibly damaging	0.80
R5802:Ltn1	UTSW	16	87,212,569 (GRCm39)	missense	probably benign	0.17
R5907:Ltn1	UTSW	16	87,178,391 (GRCm39)	missense	possibly damaging	0.94
R6180:Ltn1	UTSW	16	87,224,677 (GRCm39)	missense	probably damaging	1.00
R6194:Ltn1	UTSW	16	87,212,698 (GRCm39)	missense	probably damaging	1.00
R6257:Ltn1	UTSW	16	87,208,662 (GRCm39)	missense	possibly damaging	0.74
R6301:Ltn1	UTSW	16	87,217,194 (GRCm39)	missense	probably benign
R6481:Ltn1	UTSW	16	87,175,868 (GRCm39)	missense	probably damaging	1.00
R6525:Ltn1	UTSW	16	87,217,074 (GRCm39)	missense	probably damaging	1.00
R6958:Ltn1	UTSW	16	87,194,679 (GRCm39)	missense	probably benign
R6969:Ltn1	UTSW	16	87,212,578 (GRCm39)	missense	probably damaging	1.00
R7002:Ltn1	UTSW	16	87,220,361 (GRCm39)	missense	probably benign
R7038:Ltn1	UTSW	16	87,221,759 (GRCm39)	missense	probably damaging	1.00
R7062:Ltn1	UTSW	16	87,224,491 (GRCm39)	missense	probably damaging	0.98
R7152:Ltn1	UTSW	16	87,224,529 (GRCm39)	missense	probably damaging	1.00
R7180:Ltn1	UTSW	16	87,215,382 (GRCm39)	missense	probably damaging	0.98
R7247:Ltn1	UTSW	16	87,206,275 (GRCm39)	missense	probably benign	0.00
R7454:Ltn1	UTSW	16	87,194,700 (GRCm39)	missense	probably benign	0.03
R7471:Ltn1	UTSW	16	87,194,787 (GRCm39)	missense	probably benign
R7511:Ltn1	UTSW	16	87,205,716 (GRCm39)	missense	possibly damaging	0.63
R7691:Ltn1	UTSW	16	87,195,574 (GRCm39)	missense	probably damaging	0.99
R7702:Ltn1	UTSW	16	87,223,166 (GRCm39)	missense	probably damaging	1.00
R7761:Ltn1	UTSW	16	87,208,681 (GRCm39)	missense	probably benign
R8002:Ltn1	UTSW	16	87,212,835 (GRCm39)	missense	probably benign	0.17
R8101:Ltn1	UTSW	16	87,215,385 (GRCm39)	missense	probably damaging	1.00
R8142:Ltn1	UTSW	16	87,178,529 (GRCm39)	missense	probably benign	0.21
R8214:Ltn1	UTSW	16	87,177,691 (GRCm39)	missense	probably benign	0.02
R8674:Ltn1	UTSW	16	87,195,673 (GRCm39)	missense	probably benign
R8783:Ltn1	UTSW	16	87,207,247 (GRCm39)	missense	probably benign	0.30
R8839:Ltn1	UTSW	16	87,215,390 (GRCm39)	missense	probably damaging	1.00
R8885:Ltn1	UTSW	16	87,178,433 (GRCm39)	missense	probably damaging	1.00
R8889:Ltn1	UTSW	16	87,229,230 (GRCm39)	intron	probably benign
R8892:Ltn1	UTSW	16	87,229,230 (GRCm39)	intron	probably benign
R8919:Ltn1	UTSW	16	87,178,381 (GRCm39)	missense	probably damaging	0.98
R8970:Ltn1	UTSW	16	87,212,926 (GRCm39)	missense	probably benign
R9113:Ltn1	UTSW	16	87,224,532 (GRCm39)	missense	probably damaging	1.00
R9206:Ltn1	UTSW	16	87,197,298 (GRCm39)	missense	probably benign	0.00
R9208:Ltn1	UTSW	16	87,197,298 (GRCm39)	missense	probably benign	0.00
R9234:Ltn1	UTSW	16	87,194,089 (GRCm39)	missense	probably damaging	0.98
R9421:Ltn1	UTSW	16	87,215,375 (GRCm39)	missense	possibly damaging	0.90
R9558:Ltn1	UTSW	16	87,220,295 (GRCm39)	missense	probably benign	0.05
R9654:Ltn1	UTSW	16	87,207,227 (GRCm39)	missense	probably benign	0.00
R9738:Ltn1	UTSW	16	87,222,524 (GRCm39)	missense	probably damaging	1.00
X0028:Ltn1	UTSW	16	87,199,022 (GRCm39)	missense	probably benign	0.01
Z1177:Ltn1	UTSW	16	87,198,925 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- TATTGATGGCAAACCTGACCTGAG -3'
(R):5'- AGGAGGCTTTATACTGCTTTAACTTTG -3'

Sequencing Primer
(F):5'- GCAAACCTGACCTGAGCAGTTTTC -3'
(R):5'- CAAAGACTCAGGACTGCA -3'

Posted On

2015-05-15