Mutagenetix > Incidental Mutation

Incidental Mutation 'R9015:Lnx1'

685908

Institutional Source

Beutler Lab

Gene Symbol

Lnx1

Ensembl Gene

ENSMUSG00000029228

Gene Name

ligand of numb-protein X 1

Synonyms

MMRRC Submission

068845-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.086) question?

Stock #

R9015 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

74753108-74863573 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 74780783 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 246 (V246A)

Ref Sequence

ENSEMBL: ENSMUSP00000109159 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000039744] [ENSMUST00000087161] [ENSMUST00000113531] [ENSMUST00000117388] [ENSMUST00000117525] [ENSMUST00000121690] [ENSMUST00000127396] [ENSMUST00000153543]

AlphaFold

O70263

Predicted Effect

probably benign
Transcript: ENSMUST00000039744
AA Change: V305A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000040098
Gene: ENSMUSG00000029228
AA Change: V305A

Domain	Start	End	E-Value	Type
low complexity region	4	12	N/A	INTRINSIC
Blast:PDZ	57	164	1e-33	BLAST
PDZ	188	263	5.33e-19	SMART
PDZ	295	368	2.27e-13	SMART
PDZ	417	494	8.27e-16	SMART
PDZ	547	624	5.71e-19	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000087161
AA Change: V405A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000084405
Gene: ENSMUSG00000029228
AA Change: V405A

Domain	Start	End	E-Value	Type
RING	45	82	5.82e-6	SMART
low complexity region	97	107	N/A	INTRINSIC
Blast:PDZ	157	264	3e-33	BLAST
PDZ	288	363	5.33e-19	SMART
PDZ	395	468	2.27e-13	SMART
PDZ	517	594	8.27e-16	SMART
PDZ	647	724	5.71e-19	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000113531
AA Change: V246A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000109159
Gene: ENSMUSG00000029228
AA Change: V246A

Domain	Start	End	E-Value	Type
Blast:PDZ	2	105	2e-32	BLAST
PDZ	129	204	5.33e-19	SMART
PDZ	236	309	2.27e-13	SMART
PDZ	358	435	8.27e-16	SMART
PDZ	488	565	5.71e-19	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000117388
AA Change: V405A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000113035
Gene: ENSMUSG00000029228
AA Change: V405A

Domain	Start	End	E-Value	Type
RING	45	82	5.82e-6	SMART
low complexity region	97	107	N/A	INTRINSIC
Blast:PDZ	157	264	3e-33	BLAST
PDZ	288	363	5.33e-19	SMART
PDZ	395	468	2.27e-13	SMART
PDZ	517	594	8.27e-16	SMART
PDZ	647	724	5.71e-19	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000117525
AA Change: V305A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000113837
Gene: ENSMUSG00000029228
AA Change: V305A

Domain	Start	End	E-Value	Type
low complexity region	4	12	N/A	INTRINSIC
Blast:PDZ	57	164	1e-33	BLAST
PDZ	188	263	5.33e-19	SMART
PDZ	295	368	2.27e-13	SMART
PDZ	417	494	8.27e-16	SMART
PDZ	547	624	5.71e-19	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000121690
AA Change: V295A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000113565
Gene: ENSMUSG00000029228
AA Change: V295A

Domain	Start	End	E-Value	Type
low complexity region	4	12	N/A	INTRINSIC
PDZ	178	253	5.33e-19	SMART
PDZ	285	358	2.27e-13	SMART
PDZ	407	484	8.27e-16	SMART
PDZ	537	614	5.71e-19	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000127396

SMART Domains

Protein: ENSMUSP00000120886
Gene: ENSMUSG00000029228

Domain	Start	End	E-Value	Type
low complexity region	4	12	N/A	INTRINSIC

Predicted Effect

SMART Domains

Protein: ENSMUSP00000117935
Gene: ENSMUSG00000029228
AA Change: V88A

Domain	Start	End	E-Value	Type
PDZ	1	47	2.73e-1	SMART
PDZ	79	154	1.51e-9	SMART
PDZ	156	233	8.27e-16	SMART
SCOP:d1qaua_	274	322	3e-7	SMART
Blast:PDZ	286	322	4e-19	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000153543
AA Change: V246A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000121094
Gene: ENSMUSG00000029228
AA Change: V246A

Domain	Start	End	E-Value	Type
Blast:PDZ	2	105	9e-37	BLAST
Blast:PDZ	129	159	1e-12	BLAST

Meta Mutation Damage Score

0.0691

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

100% (93/93)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a membrane-bound protein that is involved in signal transduction and protein interactions. The encoded product is an E3 ubiquitin-protein ligase, which mediates ubiquitination and subsequent proteasomal degradation of proteins containing phosphotyrosine binding (PTB) domains. This protein may play an important role in tumorogenesis. Alternatively spliced transcript variants encoding distinct isoforms have been described. A pseudogene, which is located on chromosome 17, has been identified for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a targeted mutation exhibit an increased percentage of B1-like B cells in peritoneal lavage when compared with that of controls. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam22	T	C	5: 8,136,688 (GRCm39)		probably benign	Het
Adamtsl1	A	G	4: 86,150,847 (GRCm39)	D335G	probably damaging	Het
Adcy8	T	C	15: 64,597,206 (GRCm39)		probably benign	Het
Alas1	A	T	9: 106,113,670 (GRCm39)	I525N	probably benign	Het
Aoah	A	T	13: 21,184,197 (GRCm39)		silent	Het
Aox1	G	A	1: 58,382,851 (GRCm39)	V1044M	probably damaging	Het
Apcdd1	A	T	18: 63,083,157 (GRCm39)	Y329F	possibly damaging	Het
Arhgap10	A	C	8: 77,985,687 (GRCm39)	C727G	probably benign	Het
Arid4a	G	A	12: 71,122,168 (GRCm39)	D528N	possibly damaging	Het
Atp8a1	A	G	5: 67,887,250 (GRCm39)	V611A		Het
BC004004	T	C	17: 29,517,637 (GRCm39)	F284L	probably damaging	Het
Bean1	CT	C	8: 104,908,664 (GRCm39)		probably null	Het
Cep295	T	C	9: 15,244,264 (GRCm39)	I1397M	probably benign	Het
Cep63	A	G	9: 102,496,111 (GRCm39)	S99P	probably damaging	Het
Coq3	T	A	4: 21,899,107 (GRCm39)	S147T	probably benign	Het
Crym	A	T	7: 119,801,090 (GRCm39)	S20T	probably benign	Het
Ctr9	T	A	7: 110,643,108 (GRCm39)	N493K	probably benign	Het
Dchs2	A	G	3: 83,188,751 (GRCm39)	I1372V	possibly damaging	Het
Ddi2	G	A	4: 141,412,747 (GRCm39)	T55M	probably benign	Het
Dnah1	T	C	14: 30,986,316 (GRCm39)	M3724V	probably damaging	Het
Dst	A	G	1: 34,326,337 (GRCm39)	I4690V	probably benign	Het
Ect2l	T	C	10: 18,039,148 (GRCm39)	T429A	probably benign	Het
Eif3c	G	T	7: 126,155,538 (GRCm39)	H577N	probably damaging	Het
Erg	A	G	16: 95,162,126 (GRCm39)	S334P	possibly damaging	Het
Faf2	A	G	13: 54,796,139 (GRCm39)	S127G	probably benign	Het
Fbxl3	T	A	14: 103,329,790 (GRCm39)	T141S	possibly damaging	Het
Fbxw4	T	A	19: 45,624,874 (GRCm39)	M122L	probably benign	Het
Fgd4	T	C	16: 16,271,941 (GRCm39)	M476V	probably damaging	Het
Flvcr2	A	T	12: 85,829,779 (GRCm39)	I263F	probably benign	Het
Gadl1	A	T	9: 115,794,705 (GRCm39)	R293S	probably benign	Het
Gm11983	G	T	11: 6,787,033 (GRCm39)	F31L	unknown	Het
Gmnn	A	T	13: 24,940,638 (GRCm39)	N70K	probably benign	Het
Gpr3	A	G	4: 132,938,390 (GRCm39)	V94A	possibly damaging	Het
Greb1l	A	G	18: 10,541,675 (GRCm39)	S1141G	probably benign	Het
Helz2	A	T	2: 180,870,792 (GRCm39)	V2892E	probably damaging	Het
Hivep1	T	A	13: 42,311,849 (GRCm39)	M1363K	probably benign	Het
Hk1	T	A	10: 62,128,118 (GRCm39)	T336S	possibly damaging	Het
Hpgds	A	T	6: 65,115,229 (GRCm39)	I18N	possibly damaging	Het
Insrr	T	A	3: 87,720,910 (GRCm39)	L1056Q	probably damaging	Het
Ints10	A	G	8: 69,260,139 (GRCm39)	M288V	probably benign	Het
Itgb6	T	C	2: 60,485,032 (GRCm39)	D237G	probably damaging	Het
Kcnf1	A	G	12: 17,225,303 (GRCm39)	I306T	probably damaging	Het
Kdm3b	G	A	18: 34,963,212 (GRCm39)	G1556D	probably damaging	Het
Kif5b	A	G	18: 6,216,892 (GRCm39)	L477P	probably damaging	Het
Klf5	T	G	14: 99,540,919 (GRCm39)	*310G	probably null	Het
Ly75	C	T	2: 60,146,442 (GRCm39)	E1279K	probably benign	Het
Lztr1	T	A	16: 17,337,305 (GRCm39)	C233S	probably benign	Het
Mfsd6l	T	G	11: 68,447,536 (GRCm39)	I129S	probably benign	Het
Mrgprx2	T	A	7: 48,148,938 (GRCm39)		probably benign	Het
Ncapd2	A	T	6: 125,145,285 (GRCm39)		probably benign	Het
Or10ag53	T	A	2: 87,082,546 (GRCm39)	Y88*	probably null	Het
Or12e9	T	A	2: 87,202,485 (GRCm39)	M203K	possibly damaging	Het
Or2a25	G	T	6: 42,888,825 (GRCm39)	V123L	possibly damaging	Het
Or8g30	A	C	9: 39,230,019 (GRCm39)	V297G	probably damaging	Het
Pde6a	A	G	18: 61,397,047 (GRCm39)	H631R	probably damaging	Het
Pfkl	C	T	10: 77,824,794 (GRCm39)	G665D	probably damaging	Het
Pik3ap1	T	A	19: 41,270,430 (GRCm39)	E753V	probably damaging	Het
Pik3cd	G	T	4: 149,740,055 (GRCm39)	R502S	probably benign	Het
Piwil2	T	A	14: 70,627,984 (GRCm39)	I762L	probably benign	Het
Pkd1	T	A	17: 24,784,636 (GRCm39)	L394*	probably null	Het
Plekhb2	A	G	1: 34,916,046 (GRCm39)	D195G	probably benign	Het
Plppr5	T	C	3: 117,456,103 (GRCm39)	M208T	probably damaging	Het
Polr2i	G	A	7: 29,932,513 (GRCm39)	V115I	unknown	Het
Prkacb	T	C	3: 146,456,239 (GRCm39)	S187G	probably null	Het
Prkag3	G	T	1: 74,780,353 (GRCm39)	H437Q	probably benign	Het
Prlr	T	A	15: 10,319,352 (GRCm39)	Y94N	probably damaging	Het
Prmt6	T	C	3: 110,157,214 (GRCm39)	I358M	probably benign	Het
Psd4	A	G	2: 24,287,492 (GRCm39)	R475G		Het
Rad51b	G	A	12: 79,347,417 (GRCm39)	C27Y	probably damaging	Het
Scfd2	A	G	5: 74,691,625 (GRCm39)	L219P	probably damaging	Het
Scn5a	G	A	9: 119,381,142 (GRCm39)		probably benign	Het
Sec24d	T	C	3: 123,121,287 (GRCm39)	V391A	probably benign	Het
Selenbp2	T	A	3: 94,607,332 (GRCm39)	L251Q	probably damaging	Het
Sh3rf1	T	C	8: 61,827,202 (GRCm39)	V652A	probably benign	Het
Slc11a2	A	G	15: 100,301,186 (GRCm39)	V289A	probably benign	Het
Smim29	T	C	17: 27,783,223 (GRCm39)	D48G	probably benign	Het
Sox8	T	A	17: 25,789,135 (GRCm39)	Y121F	probably damaging	Het
Taar7a	A	T	10: 23,868,733 (GRCm39)	I216N	probably damaging	Het
Tanc1	T	A	2: 59,622,224 (GRCm39)	S448T	probably benign	Het
Tas2r119	G	A	15: 32,178,226 (GRCm39)	G264D	probably damaging	Het
Trav7-6	A	G	14: 53,954,604 (GRCm39)	K65E	probably benign	Het
Trim17	A	G	11: 58,856,057 (GRCm39)	E38G	probably damaging	Het
Trub2	A	T	2: 29,668,276 (GRCm39)		probably benign	Het
Ttn	T	A	2: 76,571,964 (GRCm39)	M26310L	probably damaging	Het
Unc13c	T	G	9: 73,453,322 (GRCm39)	I1823L	probably benign	Het
Vav2	C	A	2: 27,160,151 (GRCm39)	E728*	probably null	Het
Virma	A	G	4: 11,540,494 (GRCm39)	D1465G	probably benign	Het
Vmn2r72	T	G	7: 85,398,388 (GRCm39)	M531L	probably benign	Het
Vwa3b	G	A	1: 37,203,597 (GRCm39)	V59I	possibly damaging	Het
Xrcc1	G	A	7: 24,271,642 (GRCm39)	E542K	probably benign	Het
Zdhhc6	T	G	19: 55,287,318 (GRCm39)	T381P	probably benign	Het
Zdhhc8	T	C	16: 18,041,141 (GRCm39)	S740G	probably damaging	Het
Zfp106	T	C	2: 120,364,019 (GRCm39)	K819R	probably damaging	Het

Other mutations in Lnx1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00965:Lnx1	APN	5	74,846,378 (GRCm39)	missense	probably benign	0.00
IGL01538:Lnx1	APN	5	74,780,816 (GRCm39)	missense	possibly damaging	0.50
IGL02351:Lnx1	APN	5	74,788,027 (GRCm39)	missense	probably damaging	0.97
IGL02358:Lnx1	APN	5	74,788,027 (GRCm39)	missense	probably damaging	0.97
IGL03011:Lnx1	APN	5	74,846,420 (GRCm39)	missense	probably benign	0.02
IGL03188:Lnx1	APN	5	74,780,924 (GRCm39)	missense	probably damaging	1.00
bobcat	UTSW	5	74,846,351 (GRCm39)	missense	probably damaging	1.00
Caracal	UTSW	5	74,766,710 (GRCm39)	missense	probably damaging	1.00
R0490:Lnx1	UTSW	5	74,781,008 (GRCm39)	critical splice acceptor site	probably null
R0714:Lnx1	UTSW	5	74,768,570 (GRCm39)	splice site	probably benign
R1343:Lnx1	UTSW	5	74,758,040 (GRCm39)	missense	probably damaging	0.98
R1533:Lnx1	UTSW	5	74,780,678 (GRCm39)	missense	probably damaging	1.00
R1681:Lnx1	UTSW	5	74,846,071 (GRCm39)	missense	probably benign
R1714:Lnx1	UTSW	5	74,768,398 (GRCm39)	missense	probably null	1.00
R1727:Lnx1	UTSW	5	74,768,577 (GRCm39)	splice site	probably null
R1806:Lnx1	UTSW	5	74,766,710 (GRCm39)	missense	probably damaging	1.00
R2091:Lnx1	UTSW	5	74,780,727 (GRCm39)	missense	probably benign	0.25
R2879:Lnx1	UTSW	5	74,780,784 (GRCm39)	missense	probably benign	0.03
R2984:Lnx1	UTSW	5	74,846,083 (GRCm39)	nonsense	probably null
R3790:Lnx1	UTSW	5	74,789,027 (GRCm39)	splice site	probably benign
R3953:Lnx1	UTSW	5	74,766,750 (GRCm39)	missense	probably benign
R4509:Lnx1	UTSW	5	74,780,853 (GRCm39)	missense	probably damaging	1.00
R4510:Lnx1	UTSW	5	74,780,853 (GRCm39)	missense	probably damaging	1.00
R4511:Lnx1	UTSW	5	74,780,853 (GRCm39)	missense	probably damaging	1.00
R4575:Lnx1	UTSW	5	74,846,204 (GRCm39)	missense	probably damaging	1.00
R4583:Lnx1	UTSW	5	74,771,457 (GRCm39)	missense	probably benign	0.16
R4624:Lnx1	UTSW	5	74,821,121 (GRCm39)	intron	probably benign
R4647:Lnx1	UTSW	5	74,771,457 (GRCm39)	missense	probably benign	0.16
R4648:Lnx1	UTSW	5	74,771,457 (GRCm39)	missense	probably benign	0.16
R4877:Lnx1	UTSW	5	74,788,784 (GRCm39)	missense	probably benign	0.01
R4883:Lnx1	UTSW	5	74,768,530 (GRCm39)	missense	probably benign
R5256:Lnx1	UTSW	5	74,846,315 (GRCm39)	missense	probably damaging	1.00
R6169:Lnx1	UTSW	5	74,838,230 (GRCm39)	missense	probably damaging	1.00
R6185:Lnx1	UTSW	5	74,846,269 (GRCm39)	nonsense	probably null
R6408:Lnx1	UTSW	5	74,846,307 (GRCm39)	missense	probably damaging	1.00
R6476:Lnx1	UTSW	5	74,768,541 (GRCm39)	missense	possibly damaging	0.52
R7083:Lnx1	UTSW	5	74,788,846 (GRCm39)	missense	possibly damaging	0.94
R7085:Lnx1	UTSW	5	74,788,846 (GRCm39)	missense	possibly damaging	0.94
R7261:Lnx1	UTSW	5	74,838,175 (GRCm39)	nonsense	probably null
R7511:Lnx1	UTSW	5	74,780,972 (GRCm39)	missense	probably benign	0.01
R7574:Lnx1	UTSW	5	74,846,099 (GRCm39)	missense	probably benign	0.33
R7670:Lnx1	UTSW	5	74,846,351 (GRCm39)	missense	probably damaging	1.00
R8145:Lnx1	UTSW	5	74,846,060 (GRCm39)	missense	probably benign	0.22
R9224:Lnx1	UTSW	5	74,766,810 (GRCm39)	missense	probably benign	0.37
R9321:Lnx1	UTSW	5	74,780,991 (GRCm39)	missense	probably damaging	1.00
R9340:Lnx1	UTSW	5	74,758,584 (GRCm39)	missense	probably benign	0.01
R9704:Lnx1	UTSW	5	74,780,879 (GRCm39)	missense	probably benign	0.02
Z1177:Lnx1	UTSW	5	74,788,102 (GRCm39)	missense	possibly damaging	0.80

Predicted Primers

PCR Primer
(F):5'- ACTGAGATCTTAGGGTGACTTCTG -3'
(R):5'- GTCAACGGCATGGACATCAG -3'

Sequencing Primer
(F):5'- TAGGGTGACTTCTGACCCAC -3'
(R):5'- TCATAACTATGCCGTGCGG -3'

Posted On

2021-10-11