Mutagenetix > Incidental Mutation

Incidental Mutation 'R1557:Lrch4'

170337

Institutional Source

Beutler Lab

Gene Symbol

Lrch4

Ensembl Gene

ENSMUSG00000093445

Gene Name

leucine-rich repeats and calponin homology (CH) domain containing 4

Synonyms

LRRN4, LRN, 2810008P14Rik, 2900069C24Rik

MMRRC Submission

039596-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.173) question?

Stock #

R1557 (G1)

Quality Score

184

Status

Validated

Chromosome

Chromosomal Location

137627385-137639361 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 137635818 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 266 (D266E)

Ref Sequence

ENSEMBL: ENSMUSP00000134767 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000031734] [ENSMUST00000166099] [ENSMUST00000175968] [ENSMUST00000176011] [ENSMUST00000176667] [ENSMUST00000177545] [ENSMUST00000177477] [ENSMUST00000177466]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000031734
AA Change: D320E

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

SMART Domains

Protein: ENSMUSP00000031734
Gene: ENSMUSG00000093445
AA Change: D320E

Domain	Start	End	E-Value	Type
low complexity region	2	22	N/A	INTRINSIC
LRR	90	112	4.84e1	SMART
LRR_TYP	113	136	4.61e-5	SMART
LRR	158	180	2.63e0	SMART
LRR_TYP	181	204	1.1e-2	SMART
LRR	226	249	3.98e1	SMART
low complexity region	389	405	N/A	INTRINSIC
low complexity region	440	453	N/A	INTRINSIC
low complexity region	474	479	N/A	INTRINSIC
low complexity region	510	530	N/A	INTRINSIC
CH	533	642	9.24e-15	SMART
transmembrane domain	656	678	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000166099

SMART Domains

Protein: ENSMUSP00000127076
Gene: ENSMUSG00000079165

Domain	Start	End	E-Value	Type
Pfam:SAP25	76	261	1.8e-77	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000175968
AA Change: D266E

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

SMART Domains

Protein: ENSMUSP00000134767
Gene: ENSMUSG00000093445
AA Change: D266E

Domain	Start	End	E-Value	Type
low complexity region	3	14	N/A	INTRINSIC
LRR	36	58	4.84e1	SMART
LRR_TYP	59	82	4.61e-5	SMART
LRR	104	126	2.63e0	SMART
LRR_TYP	127	150	1.1e-2	SMART
LRR	172	195	3.98e1	SMART
low complexity region	335	351	N/A	INTRINSIC
low complexity region	386	399	N/A	INTRINSIC
low complexity region	420	425	N/A	INTRINSIC
low complexity region	456	476	N/A	INTRINSIC
CH	479	588	9.24e-15	SMART
transmembrane domain	602	624	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000176011

SMART Domains

Protein: ENSMUSP00000135133
Gene: ENSMUSG00000093445

Domain	Start	End	E-Value	Type
low complexity region	2	22	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176075

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176256

Predicted Effect

probably benign
Transcript: ENSMUST00000176667
AA Change: D320E

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

SMART Domains

Protein: ENSMUSP00000135832
Gene: ENSMUSG00000093445
AA Change: D320E

Domain	Start	End	E-Value	Type
low complexity region	2	22	N/A	INTRINSIC
LRR	90	112	4.84e1	SMART
LRR_TYP	113	136	4.61e-5	SMART
LRR	158	180	2.63e0	SMART
LRR_TYP	181	204	1.1e-2	SMART
LRR	226	249	3.98e1	SMART
low complexity region	389	405	N/A	INTRINSIC
low complexity region	440	453	N/A	INTRINSIC
low complexity region	474	479	N/A	INTRINSIC
low complexity region	510	530	N/A	INTRINSIC
CH	533	648	4.73e-12	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000177545
AA Change: D320E

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

SMART Domains

Protein: ENSMUSP00000135286
Gene: ENSMUSG00000029720
AA Change: D320E

Domain	Start	End	E-Value	Type
low complexity region	2	22	N/A	INTRINSIC
LRR	90	112	4.84e1	SMART
LRR_TYP	113	136	4.61e-5	SMART
LRR	158	180	2.63e0	SMART
LRR_TYP	181	204	1.1e-2	SMART
LRR	226	249	3.98e1	SMART
low complexity region	389	405	N/A	INTRINSIC
low complexity region	440	453	N/A	INTRINSIC
low complexity region	474	479	N/A	INTRINSIC
low complexity region	510	530	N/A	INTRINSIC
CH	533	642	9.24e-15	SMART
transmembrane domain	656	678	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176988

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000177354

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000177038

Predicted Effect

probably benign
Transcript: ENSMUST00000176768

Predicted Effect

probably benign
Transcript: ENSMUST00000176871

Predicted Effect

probably benign
Transcript: ENSMUST00000177477

SMART Domains

Protein: ENSMUSP00000135724
Gene: ENSMUSG00000093445

Domain	Start	End	E-Value	Type
low complexity region	2	22	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000177466

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.1%
3x: 98.2%
10x: 95.9%
20x: 91.1%

Validation Efficiency

96% (75/78)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that contains leucine-rich repeats (LRR) at its amino terminus and that is known to be involved in ligand binding. The carboxyl terminus may act as a membrane anchor. Identified structural elements suggest that the encoded protein resembles a receptor. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700019A02Rik	A	C	1: 53,221,025 (GRCm39)	D68E	possibly damaging	Het
Abca3	T	C	17: 24,618,954 (GRCm39)	V870A	possibly damaging	Het
Aldh3a2	A	T	11: 61,139,885 (GRCm39)	F416I	probably damaging	Het
Armc6	A	T	8: 70,678,098 (GRCm39)	L77Q	possibly damaging	Het
Asb17	A	G	3: 153,556,570 (GRCm39)	I226V	probably benign	Het
Aspm	A	G	1: 139,396,406 (GRCm39)	I862V	probably benign	Het
Atr	T	A	9: 95,753,502 (GRCm39)	D701E	probably damaging	Het
Baz1b	C	T	5: 135,247,097 (GRCm39)	L849F	possibly damaging	Het
Cbr1	T	C	16: 93,405,677 (GRCm39)	V97A	probably benign	Het
Cep295	G	A	9: 15,243,306 (GRCm39)	Q1669*	probably null	Het
Cfap54	T	C	10: 92,820,089 (GRCm39)	T1242A	possibly damaging	Het
Chrm3	T	A	13: 9,928,350 (GRCm39)	T229S	possibly damaging	Het
Cimip4	C	A	15: 78,270,474 (GRCm39)	R98M	probably damaging	Het
Cnga3	A	G	1: 37,300,066 (GRCm39)	Y300C	probably damaging	Het
Col14a1	A	C	15: 55,251,975 (GRCm39)	I544L	unknown	Het
Crocc	T	C	4: 140,752,776 (GRCm39)	E1208G	probably damaging	Het
Cyp2j8	A	T	4: 96,358,713 (GRCm39)		probably benign	Het
Dcbld2	T	C	16: 58,285,713 (GRCm39)	I624T	possibly damaging	Het
Ddah1	A	C	3: 145,597,227 (GRCm39)	I258L	probably benign	Het
Dnah6	G	A	6: 73,026,114 (GRCm39)	Q3460*	probably null	Het
Dync2h1	T	A	9: 7,140,911 (GRCm39)	D1372V	probably damaging	Het
Egln1	G	A	8: 125,674,980 (GRCm39)	R272*	probably null	Het
Elf1	A	G	14: 79,804,620 (GRCm39)	D95G	possibly damaging	Het
Fkbp5	A	G	17: 28,621,729 (GRCm39)	F374L	probably damaging	Het
Fli1	T	C	9: 32,372,540 (GRCm39)		probably benign	Het
Gabbr2	T	C	4: 46,846,436 (GRCm39)	T158A	probably damaging	Het
Gp2	A	C	7: 119,049,302 (GRCm39)	Y412D	probably damaging	Het
Hmcn1	A	G	1: 150,610,283 (GRCm39)	V1462A	possibly damaging	Het
Ide	T	C	19: 37,258,160 (GRCm39)		probably null	Het
Kalrn	T	C	16: 34,134,648 (GRCm39)	K372R	possibly damaging	Het
Kcnj16	A	G	11: 110,916,067 (GRCm39)	D243G	possibly damaging	Het
Kif7	A	G	7: 79,363,905 (GRCm39)	M1T	probably null	Het
Klri2	A	T	6: 129,709,174 (GRCm39)	L226Q	probably damaging	Het
Kremen1	T	C	11: 5,165,373 (GRCm39)		probably null	Het
Lama3	T	C	18: 12,646,788 (GRCm39)		probably benign	Het
Lmln	C	A	16: 32,908,581 (GRCm39)	R336S	probably benign	Het
Lrrc28	C	T	7: 67,209,677 (GRCm39)	R174H	probably damaging	Het
Mib1	T	A	18: 10,798,474 (GRCm39)	D778E	probably damaging	Het
Msra	T	C	14: 64,360,775 (GRCm39)	I125V	possibly damaging	Het
Or10c1	A	G	17: 37,522,244 (GRCm39)	F167L	probably damaging	Het
Or4k37	T	A	2: 111,158,964 (GRCm39)	S67T	probably damaging	Het
Or4p19	A	T	2: 88,242,555 (GRCm39)	V149E	possibly damaging	Het
Or52e18	A	G	7: 104,609,747 (GRCm39)	F64S	probably damaging	Het
Or6c75	C	A	10: 129,337,491 (GRCm39)	T246N	probably damaging	Het
Or8d23	A	G	9: 38,841,955 (GRCm39)	M163V	possibly damaging	Het
Pes1	T	A	11: 3,926,824 (GRCm39)	Y369N	probably damaging	Het
Pgam2	T	C	11: 5,751,773 (GRCm39)	D221G	possibly damaging	Het
Prl2c5	T	C	13: 13,365,265 (GRCm39)	V137A	possibly damaging	Het
Rasal1	T	A	5: 120,814,914 (GRCm39)	D721E	possibly damaging	Het
Sass6	G	T	3: 116,412,381 (GRCm39)	E385D	possibly damaging	Het
Sema5a	A	G	15: 32,460,418 (GRCm39)	R60G	probably benign	Het
Sesn1	T	C	10: 41,779,762 (GRCm39)	S399P	probably damaging	Het
Skic2	G	A	17: 35,067,398 (GRCm39)	L47F	probably damaging	Het
Slc10a2	C	T	8: 5,141,755 (GRCm39)	V210M	probably damaging	Het
Slc8a3	C	T	12: 81,362,331 (GRCm39)	G163S	probably damaging	Het
Sorbs2	T	C	8: 46,212,234 (GRCm39)		probably benign	Het
Speer4f1	T	C	5: 17,684,490 (GRCm39)	W173R	probably damaging	Het
Spon2	C	A	5: 33,374,108 (GRCm39)	G92W	probably damaging	Het
Sycp2	A	T	2: 178,037,009 (GRCm39)		probably benign	Het
Tfb1m	A	G	17: 3,605,241 (GRCm39)	V84A	probably damaging	Het
Tmem18	G	T	12: 30,637,198 (GRCm39)		probably null	Het
Tom1l1	A	G	11: 90,547,210 (GRCm39)	L290S	possibly damaging	Het
Tube1	T	G	10: 39,021,711 (GRCm39)		probably null	Het
Ugt2b35	T	A	5: 87,155,156 (GRCm39)		probably null	Het
Unc93b1	T	A	19: 3,992,403 (GRCm39)	Y269N	probably benign	Het
Usp16	T	C	16: 87,259,030 (GRCm39)		probably null	Het
Vmn1r38	A	T	6: 66,753,370 (GRCm39)	S249T	probably benign	Het
Vmn1r42	T	A	6: 89,821,733 (GRCm39)	M279L	possibly damaging	Het
Zdhhc23	T	A	16: 43,791,829 (GRCm39)	T315S	possibly damaging	Het
Zfp472	T	C	17: 33,194,900 (GRCm39)	F12L	probably benign	Het
Zfr2	T	C	10: 81,083,225 (GRCm39)	S634P	probably benign	Het

Other mutations in Lrch4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00340:Lrch4	APN	5	137,636,009 (GRCm39)	missense	possibly damaging	0.49
IGL01862:Lrch4	APN	5	137,635,271 (GRCm39)	missense	probably damaging	1.00
IGL03289:Lrch4	APN	5	137,631,839 (GRCm39)	missense	probably damaging	1.00
R0144:Lrch4	UTSW	5	137,636,805 (GRCm39)	critical splice donor site	probably null
R0724:Lrch4	UTSW	5	137,635,570 (GRCm39)	missense	probably damaging	1.00
R1330:Lrch4	UTSW	5	137,636,051 (GRCm39)	missense	probably damaging	0.99
R1694:Lrch4	UTSW	5	137,636,723 (GRCm39)	missense	probably benign	0.00
R2358:Lrch4	UTSW	5	137,636,810 (GRCm39)	unclassified	probably benign
R3755:Lrch4	UTSW	5	137,635,992 (GRCm39)	missense	probably damaging	1.00
R3756:Lrch4	UTSW	5	137,635,992 (GRCm39)	missense	probably damaging	1.00
R4608:Lrch4	UTSW	5	137,637,408 (GRCm39)	nonsense	probably null
R5056:Lrch4	UTSW	5	137,635,113 (GRCm39)	missense	probably damaging	1.00
R5114:Lrch4	UTSW	5	137,636,179 (GRCm39)	missense	probably benign
R5181:Lrch4	UTSW	5	137,627,665 (GRCm39)	missense	probably damaging	1.00
R5325:Lrch4	UTSW	5	137,636,168 (GRCm39)	missense	probably damaging	1.00
R5430:Lrch4	UTSW	5	137,636,795 (GRCm39)	missense	possibly damaging	0.46
R5712:Lrch4	UTSW	5	137,636,188 (GRCm39)	missense	possibly damaging	0.57
R5846:Lrch4	UTSW	5	137,631,919 (GRCm39)	missense	probably damaging	1.00
R5909:Lrch4	UTSW	5	137,632,127 (GRCm39)	missense	possibly damaging	0.87
R7319:Lrch4	UTSW	5	137,637,977 (GRCm39)	missense
R7525:Lrch4	UTSW	5	137,637,727 (GRCm39)	missense	probably damaging	1.00
R7761:Lrch4	UTSW	5	137,638,025 (GRCm39)	missense
R7848:Lrch4	UTSW	5	137,632,116 (GRCm39)	missense	probably damaging	1.00
R8209:Lrch4	UTSW	5	137,637,997 (GRCm39)	missense
R8226:Lrch4	UTSW	5	137,637,997 (GRCm39)	missense
R8713:Lrch4	UTSW	5	137,638,125 (GRCm39)	nonsense	probably null
R9361:Lrch4	UTSW	5	137,635,076 (GRCm39)	missense	probably damaging	1.00
R9372:Lrch4	UTSW	5	137,631,953 (GRCm39)	missense	possibly damaging	0.70
R9440:Lrch4	UTSW	5	137,636,051 (GRCm39)	missense	probably damaging	0.99
R9752:Lrch4	UTSW	5	137,636,218 (GRCm39)	missense	probably benign
R9796:Lrch4	UTSW	5	137,635,269 (GRCm39)	missense	probably damaging	0.99
RF009:Lrch4	UTSW	5	137,635,805 (GRCm39)	critical splice acceptor site	probably null

Predicted Primers

PCR Primer
(F):5'- CCAGCCCTGCCGAAGATTTATTTCC -3'
(R):5'- AGTCAATCTGCTCCAGGTCTCCATC -3'

Sequencing Primer
(F):5'- GGACTGGGGACTCTATACCTAAC -3'
(R):5'- GTCTCCATCGCCTGCAAG -3'

Posted On

2014-04-13