Mutagenetix > Incidental Mutation

Incidental Mutation 'R5288:Ltn1'

424547

Institutional Source

Beutler Lab

Gene Symbol

Ltn1

Ensembl Gene

ENSMUSG00000052299

Gene Name

listerin E3 ubiquitin protein ligase 1

Synonyms

4930528H02Rik, Rnf160, Zfp294, Listerin

MMRRC Submission

042842-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5288 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

87376651-87432612 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 87416011 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Arginine at position 554 (K554R)

Ref Sequence

ENSEMBL: ENSMUSP00000038775 (fasta)

Gene Model

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

AlphaFold

Q6A009

Predicted Effect

possibly damaging
Transcript: ENSMUST00000039449
AA Change: K554R

PolyPhen 2 Score 0.795 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000038775
Gene: ENSMUSG00000052299
AA Change: K554R

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: K554R

PolyPhen 2 Score 0.785 (Sensitivity: 0.85; Specificity: 0.93)

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.1%
20x: 94.7%

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: 113 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3110001I22Rik	T	G	16: 13,677,758	N240K	probably benign	Het
Abcc12	A	T	8: 86,566,539	Y7N	probably damaging	Het
Adcy1	A	C	11: 7,161,351	I881L	probably benign	Het
Aftph	T	C	11: 20,726,994	D205G	probably damaging	Het
Aldh7a1	T	A	18: 56,534,253	N316Y	possibly damaging	Het
Ankrd36	A	G	11: 5,689,340		probably benign	Het
C87414	C	T	5: 93,637,748	M224I	possibly damaging	Het
Ccdc88a	T	G	11: 29,498,416	N1465K	possibly damaging	Het
Ccpg1	G	A	9: 73,013,044	S647N	probably benign	Het
Cep70	T	A	9: 99,281,075	L325Q	probably damaging	Het
Cfap46	A	G	7: 139,613,507		probably null	Het
Cftr	C	T	6: 18,226,129	Q359*	probably null	Het
Chrne	A	T	11: 70,615,087	N457K	possibly damaging	Het
Cntn2	A	G	1: 132,523,677	I438T	probably benign	Het
Cntn4	T	C	6: 106,181,804	L10P	possibly damaging	Het
Copg1	G	T	6: 87,890,207	M87I	possibly damaging	Het
Cyfip1	A	T	7: 55,925,135	M1045L	possibly damaging	Het
Cyp2c29	C	T	19: 39,330,372	P432L	probably damaging	Het
Dcaf11	T	A	14: 55,563,376	D96E	probably damaging	Het
Dmxl2	A	G	9: 54,378,757	S2715P	probably benign	Het
Dnhd1	G	A	7: 105,714,437	E4069K	possibly damaging	Het
Dpy19l4	T	A	4: 11,289,721	N330I	probably damaging	Het
Dpy19l4	G	T	4: 11,304,014	A132D	probably damaging	Het
Duox2	A	G	2: 122,295,136	V330A	probably benign	Het
Dusp11	T	C	6: 85,947,605	*322W	probably null	Het
Dusp8	T	A	7: 142,089,993	Q61L	possibly damaging	Het
Eml3	G	A	19: 8,939,274	G720S	probably damaging	Het
F11	A	G	8: 45,246,796	S418P	probably damaging	Het
Fam91a1	G	A	15: 58,448,394	S645N	probably benign	Het
Fat2	G	A	11: 55,267,656	T3412I	probably benign	Het
Fbxo38	A	G	18: 62,540,971	M13T	probably benign	Het
Fbxo48	G	T	11: 16,954,329	L160F	possibly damaging	Het
Gm10134	T	A	2: 28,506,360		probably benign	Het
Gm11787	T	C	4: 3,511,795		noncoding transcript	Het
Gm14085	C	A	2: 122,522,778	L480I	probably benign	Het
Gpatch8	A	T	11: 102,508,227		probably null	Het
Gucy2g	G	A	19: 55,215,116	A750V	probably damaging	Het
Hephl1	T	C	9: 15,076,854	T653A	possibly damaging	Het
Herc3	T	A	6: 58,874,278	M504K	probably damaging	Het
Hmcn2	A	G	2: 31,460,321	T5077A	probably benign	Het
Ifitm3	T	C	7: 141,010,641	N2S	probably benign	Het
Ighe	T	C	12: 113,271,472	H356R	probably benign	Het
Ighv10-3	T	A	12: 114,523,505	M99L	probably benign	Het
Izumo4	C	A	10: 80,702,805	C30*	probably null	Het
Jag1	A	T	2: 137,095,544	H303Q	possibly damaging	Het
Kif24	T	C	4: 41,395,373	E500G	probably benign	Het
Kng1	A	T	16: 23,079,092	D414V	probably damaging	Het
Loxhd1	A	C	18: 77,363,612	D410A	probably damaging	Het
Ly75	A	G	2: 60,303,641	C1547R	probably damaging	Het
Ms4a6d	A	T	19: 11,587,136	S124T	possibly damaging	Het
Mtfr2	A	G	10: 20,357,702	D339G	probably damaging	Het
Myh10	T	A	11: 68,801,608	L1369Q	probably damaging	Het
Myh11	A	T	16: 14,208,008	V1366D	possibly damaging	Het
Nadsyn1	A	G	7: 143,803,286	V491A	possibly damaging	Het
Nav3	T	C	10: 109,853,105	N437S	probably benign	Het
Ncf1	A	G	5: 134,221,805	L373P	probably damaging	Het
Neb	A	T	2: 52,189,861	I85N	probably damaging	Het
Nktr	A	G	9: 121,748,593	K576E	probably benign	Het
Nmur2	T	A	11: 56,040,214	I224F	probably damaging	Het
Oas3	A	G	5: 120,756,990	F978S	probably damaging	Het
Olfr1115	C	T	2: 87,252,483	P182L	probably benign	Het
Olfr1331	T	C	4: 118,869,575	S264P	probably damaging	Het
Olfr330	A	T	11: 58,529,482	M168K	probably damaging	Het
Olfr457	T	A	6: 42,471,252	I309F	probably benign	Het
Olfr484	T	C	7: 108,125,168	T32A	probably benign	Het
Pcyox1	A	T	6: 86,392,354		probably null	Het
Pdcd7	G	A	9: 65,358,692	W477*	probably null	Het
Pitpnm1	T	C	19: 4,103,435	F197S	probably damaging	Het
Plce1	C	A	19: 38,760,091	N1755K	probably damaging	Het
Pnpla7	C	A	2: 25,041,019	P882Q	probably damaging	Het
Pold2	A	G	11: 5,876,760	L58P	probably damaging	Het
Pomt1	C	G	2: 32,244,299	Y277*	probably null	Het
Pou4f2	A	G	8: 78,436,329	Y26H	unknown	Het
Ppm1e	A	T	11: 87,358,551	L118Q	possibly damaging	Het
Prdx2	T	A	8: 84,971,673	Y164*	probably null	Het
Prkra	T	G	2: 76,639,278	T146P	probably damaging	Het
Prpf8	A	G	11: 75,495,799	D1038G	probably damaging	Het
Rab4a	A	T	8: 123,827,374	I16L	probably benign	Het
Rai2	A	G	X: 161,778,640	N363S	probably benign	Het
Ranbp17	A	T	11: 33,219,241	V991D	possibly damaging	Het
Rimbp2	G	A	5: 128,788,592	T557M	probably benign	Het
Rmi1	G	A	13: 58,409,466	G510R	probably damaging	Het
Sdad1	A	G	5: 92,286,825	*687Q	probably null	Het
Sema6d	T	C	2: 124,664,246	L720P	probably damaging	Het
Setx	T	G	2: 29,134,033		probably null	Het
Sgsm3	T	C	15: 81,007,999	V256A	probably benign	Het
Soga3	A	G	10: 29,196,770	D686G	probably benign	Het
Sppl2c	T	A	11: 104,187,301	I309K	possibly damaging	Het
Stard9	A	G	2: 120,700,630	E2456G	probably damaging	Het
Strn3	C	G	12: 51,648,020	R320P	probably damaging	Het
Supv3l1	A	T	10: 62,430,596	N600K	possibly damaging	Het
Syne2	T	A	12: 76,099,338	S6377T	possibly damaging	Het
Tas2r123	A	T	6: 132,847,227	H29L	probably benign	Het
Tbl3	C	T	17: 24,705,970	V52M	possibly damaging	Het
Tbp	A	G	17: 15,507,347	I145V	probably benign	Het
Tcf20	A	T	15: 82,855,709	S514T	possibly damaging	Het
Tgm4	A	G	9: 123,056,494	Y367C	probably damaging	Het
Tle1	C	T	4: 72,141,844	V258M	probably damaging	Het
Tln1	C	T	4: 43,540,661	V1447I	probably benign	Het
Tnfrsf11b	C	T	15: 54,278,226	A8T	probably benign	Het
Trim80	A	T	11: 115,448,017	T558S	probably benign	Het
Trmt6	C	A	2: 132,808,783	A302S	probably benign	Het
Tsen15	C	T	1: 152,383,380	V76I	probably damaging	Het
Ttc17	A	T	2: 94,303,640	W1067R	probably damaging	Het
Ucn3	A	T	13: 3,941,474	F59L	probably benign	Het
Ulk3	T	A	9: 57,590,740	I108N	possibly damaging	Het
Vmn2r94	A	C	17: 18,244,466	Y521D	probably damaging	Het
Vps45	T	C	3: 96,057,774	M1V	probably null	Het
Vta1	C	A	10: 14,705,399	L21F	probably damaging	Het
Zdhhc21	C	T	4: 82,847,692	G2D	probably damaging	Het
Zfp169	A	T	13: 48,490,275	C459S	possibly damaging	Het
Zfp90	C	T	8: 106,425,368	T571M	probably damaging	Het
Zswim8	A	T	14: 20,718,871	N1119I	possibly damaging	Het

Other mutations in Ltn1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00328:Ltn1	APN	16	87418490	missense	probably benign	0.03
IGL01139:Ltn1	APN	16	87416009	missense	probably benign	0.04
IGL01359:Ltn1	APN	16	87405693	splice site	probably benign
IGL01503:Ltn1	APN	16	87420807	critical splice donor site	probably benign
IGL01529:Ltn1	APN	16	87381471	missense	probably benign	0.00
IGL02437:Ltn1	APN	16	87398001	missense	probably benign	0.04
IGL02658:Ltn1	APN	16	87415774	missense	probably damaging	1.00
IGL02890:Ltn1	APN	16	87409297	splice site	probably null
IGL02899:Ltn1	APN	16	87382659	missense	probably benign	0.34
IGL02902:Ltn1	APN	16	87379805	missense	possibly damaging	0.70
IGL03128:Ltn1	APN	16	87415944	missense	probably benign	0.00
IGL03392:Ltn1	APN	16	87425611	missense	probably damaging	1.00
IGL03046:Ltn1	UTSW	16	87405621	missense	probably benign	0.10
PIT4305001:Ltn1	UTSW	16	87420323	missense	probably damaging	1.00
PIT4366001:Ltn1	UTSW	16	87380840	nonsense	probably null
R0126:Ltn1	UTSW	16	87425640	missense	probably benign	0.00
R0164:Ltn1	UTSW	16	87405519	splice site	probably benign
R0165:Ltn1	UTSW	16	87405519	splice site	probably benign
R0280:Ltn1	UTSW	16	87397838	missense	probably damaging	1.00
R0565:Ltn1	UTSW	16	87416010	missense	probably benign	0.01
R0733:Ltn1	UTSW	16	87412507	missense	probably benign	0.01
R1034:Ltn1	UTSW	16	87397137	splice site	probably null
R1252:Ltn1	UTSW	16	87416030	missense	probably benign	0.00
R1524:Ltn1	UTSW	16	87381556	missense	probably damaging	1.00
R1746:Ltn1	UTSW	16	87411781	missense	possibly damaging	0.86
R1826:Ltn1	UTSW	16	87415616	missense	probably damaging	1.00
R1831:Ltn1	UTSW	16	87400146	missense	possibly damaging	0.94
R1839:Ltn1	UTSW	16	87416264	nonsense	probably null
R1860:Ltn1	UTSW	16	87416343	missense	probably benign	0.06
R1997:Ltn1	UTSW	16	87381637	missense	probably damaging	1.00
R2109:Ltn1	UTSW	16	87415642	missense	probably benign	0.03
R2134:Ltn1	UTSW	16	87382713	missense	probably damaging	1.00
R2135:Ltn1	UTSW	16	87382713	missense	probably damaging	1.00
R2193:Ltn1	UTSW	16	87427647	missense	probably damaging	1.00
R2307:Ltn1	UTSW	16	87432424	critical splice donor site	probably null
R2376:Ltn1	UTSW	16	87420807	critical splice donor site	probably null
R3054:Ltn1	UTSW	16	87404073	missense	probably benign	0.32
R3404:Ltn1	UTSW	16	87416215	missense	probably damaging	0.98
R3405:Ltn1	UTSW	16	87416215	missense	probably damaging	0.98
R3618:Ltn1	UTSW	16	87420899	missense	probably damaging	1.00
R4065:Ltn1	UTSW	16	87416230	missense	possibly damaging	0.84
R4066:Ltn1	UTSW	16	87416230	missense	possibly damaging	0.84
R4067:Ltn1	UTSW	16	87416230	missense	possibly damaging	0.84
R4288:Ltn1	UTSW	16	87397988	missense	possibly damaging	0.57
R4436:Ltn1	UTSW	16	87405614	missense	probably benign	0.17
R4535:Ltn1	UTSW	16	87426286	missense	probably damaging	1.00
R4581:Ltn1	UTSW	16	87402024	critical splice donor site	probably null
R4669:Ltn1	UTSW	16	87418487	missense	possibly damaging	0.90
R4715:Ltn1	UTSW	16	87418494	missense	probably damaging	0.98
R4830:Ltn1	UTSW	16	87379694	missense	probably damaging	1.00
R4887:Ltn1	UTSW	16	87398809	nonsense	probably null
R4961:Ltn1	UTSW	16	87397791	missense	probably benign
R4992:Ltn1	UTSW	16	87405587	missense	possibly damaging	0.70
R5073:Ltn1	UTSW	16	87427740	missense	probably damaging	0.99
R5802:Ltn1	UTSW	16	87415681	missense	probably benign	0.17
R5907:Ltn1	UTSW	16	87381503	missense	possibly damaging	0.94
R6180:Ltn1	UTSW	16	87427789	missense	probably damaging	1.00
R6194:Ltn1	UTSW	16	87415810	missense	probably damaging	1.00
R6257:Ltn1	UTSW	16	87411774	missense	possibly damaging	0.74
R6301:Ltn1	UTSW	16	87420306	missense	probably benign
R6481:Ltn1	UTSW	16	87378980	missense	probably damaging	1.00
R6525:Ltn1	UTSW	16	87420186	missense	probably damaging	1.00
R6958:Ltn1	UTSW	16	87397791	missense	probably benign
R6969:Ltn1	UTSW	16	87415690	missense	probably damaging	1.00
R7002:Ltn1	UTSW	16	87423473	missense	probably benign
R7038:Ltn1	UTSW	16	87424871	missense	probably damaging	1.00
R7062:Ltn1	UTSW	16	87427603	missense	probably damaging	0.98
R7152:Ltn1	UTSW	16	87427641	missense	probably damaging	1.00
R7180:Ltn1	UTSW	16	87418494	missense	probably damaging	0.98
R7247:Ltn1	UTSW	16	87409387	missense	probably benign	0.00
R7454:Ltn1	UTSW	16	87397812	missense	probably benign	0.03
R7471:Ltn1	UTSW	16	87397899	missense	probably benign
R7511:Ltn1	UTSW	16	87408828	missense	possibly damaging	0.63
R7691:Ltn1	UTSW	16	87398686	missense	probably damaging	0.99
R7702:Ltn1	UTSW	16	87426278	missense	probably damaging	1.00
R7761:Ltn1	UTSW	16	87411793	missense	probably benign
R8002:Ltn1	UTSW	16	87415947	missense	probably benign	0.17
R8101:Ltn1	UTSW	16	87418497	missense	probably damaging	1.00
R8142:Ltn1	UTSW	16	87381641	missense	probably benign	0.21
R8214:Ltn1	UTSW	16	87380803	missense	probably benign	0.02
R8674:Ltn1	UTSW	16	87398785	missense	probably benign
R8783:Ltn1	UTSW	16	87410359	missense	probably benign	0.30
R8839:Ltn1	UTSW	16	87418502	missense	probably damaging	1.00
R8885:Ltn1	UTSW	16	87381545	missense	probably damaging	1.00
R8889:Ltn1	UTSW	16	87432342	intron	probably benign
R8892:Ltn1	UTSW	16	87432342	intron	probably benign
R8919:Ltn1	UTSW	16	87381493	missense	probably damaging	0.98
R8970:Ltn1	UTSW	16	87416038	missense	probably benign
R9113:Ltn1	UTSW	16	87427644	missense	probably damaging	1.00
R9206:Ltn1	UTSW	16	87400410	missense	probably benign	0.00
R9208:Ltn1	UTSW	16	87400410	missense	probably benign	0.00
R9234:Ltn1	UTSW	16	87397201	missense	probably damaging	0.98
R9421:Ltn1	UTSW	16	87418487	missense	possibly damaging	0.90
R9558:Ltn1	UTSW	16	87423407	missense	probably benign	0.05
R9654:Ltn1	UTSW	16	87410339	missense	probably benign	0.00
R9738:Ltn1	UTSW	16	87425636	missense	probably damaging	1.00
X0028:Ltn1	UTSW	16	87402134	missense	probably benign	0.01
Z1177:Ltn1	UTSW	16	87402037	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- GACTTCCGCTCGTTGACAAAG -3'
(R):5'- CCTGGAGCTGTTTACAACTTGG -3'

Sequencing Primer
(F):5'- TCCGCTCGTTGACAAAGCTAATG -3'
(R):5'- CAACTTGGAGAACGTTCTGC -3'

Posted On

2016-08-04