Mutagenetix > Incidental Mutations

Incidental Mutation 'R7525:Lrch4'

582912

Institutional Source

Beutler Lab

Gene Symbol

Lrch4

Ensembl Gene

ENSMUSG00000093445

Gene Name

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

Synonyms

2810008P14Rik, LRN, LRRN4, 2900069C24Rik, SAP25

Accession Numbers

Is this an essential gene?

Possibly non essential (E-score: 0.321) question?

Stock #

R7525 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

137629121-137641099 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 137639465 bp

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 582 (I582N)

Ref Sequence

ENSEMBL: ENSMUSP00000031734 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000031734] [ENSMUST00000057314] [ENSMUST00000166099] [ENSMUST00000175968] [ENSMUST00000176667] [ENSMUST00000177466] [ENSMUST00000177477] [ENSMUST00000177545] [ENSMUST00000196511]

Predicted Effect

probably damaging
Transcript: ENSMUST00000031734
AA Change: I582N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000031734
Gene: ENSMUSG00000093445
AA Change: I582N

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: ENSMUST00000057314

SMART Domains

Protein: ENSMUSP00000060844
Gene: ENSMUSG00000047182

Domain	Start	End	E-Value	Type
PH	33	135	4.46e-11	SMART
IRS	159	272	1.18e-30	SMART
PTBI	159	272	7.23e-55	SMART

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 damaging
Transcript: ENSMUST00000175968
AA Change: I528N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000134767
Gene: ENSMUSG00000093445
AA Change: I528N

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 damaging
Transcript: ENSMUST00000176667
AA Change: I582N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000135832
Gene: ENSMUSG00000093445
AA Change: I582N

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: ENSMUST00000176871

Predicted Effect

probably benign
Transcript: ENSMUST00000177466

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 damaging
Transcript: ENSMUST00000177545
AA Change: I582N

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000135286
Gene: ENSMUSG00000029720
AA Change: I582N

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: ENSMUST00000196511

SMART Domains

Protein: ENSMUSP00000142730
Gene: ENSMUSG00000047182

Domain	Start	End	E-Value	Type
PH	33	135	4.46e-11	SMART
IRS	159	272	1.18e-30	SMART
PTBI	159	272	7.23e-55	SMART

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

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: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2900026A02Rik	T	C	5: 113,183,355	T998A	probably damaging	Het
AI314180	A	G	4: 58,847,038	I508T	possibly damaging	Het
Akap9	C	G	5: 3,968,745	H1109D	probably benign	Het
Akt3	T	A	1: 177,020,107	K465*	probably null	Het
Ankar	T	C	1: 72,688,641	D371G	probably benign	Het
Ankib1	T	G	5: 3,755,734	N178H	possibly damaging	Het
Arhgap10	A	G	8: 77,420,070		probably null	Het
Arhgef4	A	G	1: 34,809,704	D286G	probably damaging	Het
Bsdc1	A	T	4: 129,461,684		probably benign	Het
Camk4	T	C	18: 33,185,032	V414A	probably benign	Het
Cyp2d9	T	A	15: 82,454,092	V139E	possibly damaging	Het
Dhrs13	C	A	11: 78,032,434	N21K	unknown	Het
Dopey1	C	T	9: 86,506,290	A439V	probably damaging	Het
Dpy19l4	G	A	4: 11,317,160	Q13*	probably null	Het
Eif2ak1	T	C	5: 143,886,898	S388P	probably damaging	Het
Emilin2	T	C	17: 71,274,979	S251G	probably benign	Het
Eml4	T	A	17: 83,445,950	L350Q	probably damaging	Het
Fblim1	A	T	4: 141,590,080	L98H	probably damaging	Het
Fcrl6	T	A	1: 172,597,672	N264I	probably benign	Het
Gm13124	A	G	4: 144,565,010	F42S	probably damaging	Het
Gzme	A	C	14: 56,119,333	D57E	probably benign	Het
H2-D1	A	G	17: 35,265,933	T257A	probably damaging	Het
Hectd4	C	A	5: 121,343,665	D3092E	possibly damaging	Het
Hrc	A	G	7: 45,336,379	E318G	probably benign	Het
Hspbp1	A	G	7: 4,663,436	L315P	probably damaging	Het
Insr	A	T	8: 3,192,642	Y591N	probably damaging	Het
Lrit2	A	G	14: 37,072,493	K505E	possibly damaging	Het
Lrp1b	A	T	2: 40,657,416	N4251K		Het
Mfsd13a	T	C	19: 46,369,277	F290S	probably damaging	Het
Mgam	T	G	6: 40,766,020	N1791K	probably benign	Het
Mroh7	A	T	4: 106,709,702	I450N	probably benign	Het
Mylk	G	A	16: 34,988,987	M1771I	probably benign	Het
Olfr1335	A	T	4: 118,809,494	F123L	probably damaging	Het
Olfr26	A	T	9: 38,855,238	M59L	possibly damaging	Het
Olfr612	A	T	7: 103,539,131	C34*	probably null	Het
Olfr972	T	A	9: 39,874,139	L288*	probably null	Het
Parp14	A	T	16: 35,857,491	H702Q	probably benign	Het
Pcdhga1	T	C	18: 37,662,228	L95P	probably damaging	Het
Pcsk5	T	C	19: 17,642,590	T373A	probably damaging	Het
Pdzph1	A	G	17: 58,967,341	V836A	possibly damaging	Het
Pgap1	T	A	1: 54,530,922	N322I	probably benign	Het
Pikfyve	C	T	1: 65,244,426	R741*	probably null	Het
Pip4k2c	A	G	10: 127,208,904	S80P	probably damaging	Het
Plekhh3	A	G	11: 101,166,619	F271L	probably damaging	Het
Prkdc	A	T	16: 15,672,327	Y565F	probably damaging	Het
Prom2	T	C	2: 127,532,781	R612G	probably benign	Het
Psap	T	C	10: 60,299,474	V303A	probably benign	Het
Ptch1	C	T	13: 63,511,714	R1375H	probably benign	Het
Rsf1	C	CGGCGGCGGG	7: 97,579,935		probably benign	Het
Slc24a3	A	C	2: 145,613,530	K446N	probably benign	Het
Slc39a12	T	A	2: 14,494,461	M661K	probably benign	Het
Slc6a16	T	C	7: 45,259,113	L39P	probably benign	Het
Syne1	T	G	10: 5,185,559		probably null	Het
Taar8c	T	C	10: 24,101,866	N16S	probably benign	Het
Tmem98	A	G	11: 80,817,518	T105A	probably damaging	Het
Tmub1	T	A	5: 24,446,013	Y216F	probably damaging	Het
Trim16	T	G	11: 62,820,754	C84G	probably damaging	Het
Ttn	T	A	2: 76,731,229	K28978*	probably null	Het
Usp38	A	G	8: 81,014,246	V64A	probably damaging	Het
Vmn2r63	A	T	7: 42,926,982	F469Y	possibly damaging	Het
Vmn2r74	A	G	7: 85,961,302	W61R	probably benign	Het
Whamm	G	T	7: 81,593,850	G607C	probably damaging	Het
Xkr6	G	T	14: 63,819,161	V430F	probably benign	Het
Zfp398	A	G	6: 47,865,818	D268G	probably benign	Het

Other mutations in Lrch4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00340:Lrch4	APN	5	137637747	missense	possibly damaging	0.49
IGL01862:Lrch4	APN	5	137637009	missense	probably damaging	1.00
IGL03289:Lrch4	APN	5	137633577	missense	probably damaging	1.00
R0144:Lrch4	UTSW	5	137638543	critical splice donor site	probably null
R0724:Lrch4	UTSW	5	137637308	missense	probably damaging	1.00
R1330:Lrch4	UTSW	5	137637789	missense	probably damaging	0.99
R1557:Lrch4	UTSW	5	137637556	missense	probably benign	0.00
R1694:Lrch4	UTSW	5	137638461	missense	probably benign	0.00
R2358:Lrch4	UTSW	5	137638548	unclassified	probably benign
R3755:Lrch4	UTSW	5	137637730	missense	probably damaging	1.00
R3756:Lrch4	UTSW	5	137637730	missense	probably damaging	1.00
R4608:Lrch4	UTSW	5	137639146	nonsense	probably null
R5056:Lrch4	UTSW	5	137636851	missense	probably damaging	1.00
R5114:Lrch4	UTSW	5	137637917	missense	probably benign
R5181:Lrch4	UTSW	5	137629403	missense	probably damaging	1.00
R5325:Lrch4	UTSW	5	137637906	missense	probably damaging	1.00
R5430:Lrch4	UTSW	5	137638533	missense	possibly damaging	0.46
R5712:Lrch4	UTSW	5	137637926	missense	possibly damaging	0.57
R5846:Lrch4	UTSW	5	137633657	missense	probably damaging	1.00
R5909:Lrch4	UTSW	5	137633865	missense	possibly damaging	0.87
R7319:Lrch4	UTSW	5	137639715	missense
R7761:Lrch4	UTSW	5	137639763	missense
RF009:Lrch4	UTSW	5	137637543	critical splice acceptor site	probably null

Predicted Primers

PCR Primer
(F):5'- TGATATTCACGGAGGCCTGG -3'
(R):5'- CGACAGGCTTCTAGGAAACTC -3'

Sequencing Primer
(F):5'- CACAACTCCTGTTATCGAGGAGG -3'
(R):5'- GGCTTCTAGGAAACTCTCGAC -3'

Posted On

2019-10-17