Mutagenetix > Incidental Mutation

Incidental Mutation 'R9440:Lrch4'

713580

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

MMRRC Submission

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.207) question?

Stock #

R9440 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

137629121-137641099 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 137637789 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glutamine at position 368 (R368Q)

Ref Sequence

ENSEMBL: ENSMUSP00000135286 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000031734
AA Change: R368Q

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000031734
Gene: ENSMUSG00000093445
AA Change: R368Q

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: R314Q

PolyPhen 2 Score 0.385 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000134767
Gene: ENSMUSG00000093445
AA Change: R314Q

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

possibly damaging
Transcript: ENSMUST00000176667
AA Change: R368Q

PolyPhen 2 Score 0.615 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000135832
Gene: ENSMUSG00000093445
AA Change: R368Q

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: ENSMUST00000176768

Predicted Effect

probably benign
Transcript: ENSMUST00000176871

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176988

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000177038

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000177354

Predicted Effect

probably damaging
Transcript: ENSMUST00000177545
AA Change: R368Q

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000135286
Gene: ENSMUSG00000029720
AA Change: R368Q

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: 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

Meta Mutation Damage Score

0.1594

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.3%

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: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110004E09Rik	A	T	16: 90,929,944	V116E	probably benign	Het
Abca17	G	A	17: 24,280,478	T1359M	probably benign	Het
Acacb	T	A	5: 114,246,024	C2205S	possibly damaging	Het
Akap3	A	G	6: 126,864,628	E70G	probably benign	Het
Aldh1a3	C	A	7: 66,419,244		probably null	Het
Asb4	A	G	6: 5,429,817	I352M	probably benign	Het
Bach1	C	G	16: 87,719,715	S381R	probably benign	Het
BC034090	A	G	1: 155,226,215	L101P	probably benign	Het
Bms1	A	T	6: 118,405,256	D440E	probably benign	Het
Bpifb6	A	T	2: 153,905,994	D191V	probably benign	Het
Cfd	T	C	10: 79,890,982		probably null	Het
Cnot3	G	A	7: 3,653,561	E252K	probably damaging	Het
Col6a3	T	C	1: 90,779,346	D2622G	unknown	Het
Crybg2	T	C	4: 134,074,291	S612P	probably benign	Het
Cyp4b1	T	C	4: 115,636,384	K167R	probably damaging	Het
Gbp3	T	C	3: 142,566,574	V279A	possibly damaging	Het
Gipc2	T	C	3: 152,128,069	T192A	possibly damaging	Het
Gm3285	T	C	10: 77,862,077	V20A		Het
Gm35339	T	C	15: 76,360,864	S1176P		Het
Gorasp2	T	C	2: 70,711,125		probably null	Het
Gpr179	A	G	11: 97,338,489	S947P	probably benign	Het
Klra5	C	A	6: 129,906,723	W147L	possibly damaging	Het
Mamdc4	A	G	2: 25,565,588	V876A	probably benign	Het
Marf1	A	C	16: 14,120,332	D1433E	probably benign	Het
Mcm4	A	T	16: 15,635,311	C171*	probably null	Het
Micall1	C	T	15: 79,126,959	P510S		Het
Morc3	A	G	16: 93,853,087		probably null	Het
Mrpl28	G	T	17: 26,126,292	V229F	possibly damaging	Het
Mrps33	A	T	6: 39,805,430	Y52*	probably null	Het
Mybphl	T	C	3: 108,374,886	I144T	probably benign	Het
Myom1	A	G	17: 71,126,334	M1657V	probably benign	Het
Ogfr	AGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCAAAAGGCCAGGTGGAGCCAGAGGACCCAAAAGGCCAGGTGGGGCCAGAAGACCCAAAAGGCCAGGTGGGGCCAGAGGACCCAAAAGGCCAGGTGGGGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGGGGCCAGAG	AGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCAAAAGGCCAGGTGGAGCCAGAGGACCCAAAAGGCCAGGTGGGGCCAGAAGACCCAAAAGGCCAGGTGGGGCCAGAGGACCCAAAAGGCCAGGTGGGGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGGGGCCAGAG	2: 180,595,057		probably benign	Het
Olfr492	A	G	7: 108,322,830	I282T	probably benign	Het
Peg10	T	TCCG	6: 4,756,451		probably benign	Het
Plxna1	T	C	6: 89,341,930	K637R	probably benign	Het
Prob1	G	T	18: 35,653,165	L679I	possibly damaging	Het
Sgms2	C	A	3: 131,325,069	C255F	probably damaging	Het
Slc17a9	T	C	2: 180,741,297	C399R	probably benign	Het
Smc4	T	A	3: 69,008,122		probably null	Het
St14	A	G	9: 31,096,549	L578P	probably damaging	Het
Tcaf3	A	T	6: 42,596,972	L102*	probably null	Het
Tex15	A	G	8: 33,582,245	T2607A	possibly damaging	Het
Trav15-2-dv6-2	T	A	14: 53,649,475		probably benign	Het
Trip4	T	C	9: 65,852,952		probably null	Het
Ttf1	A	G	2: 29,065,697	I358V	probably benign	Het
Uroc1	C	A	6: 90,345,371	S292R	possibly damaging	Het
Vmn1r5	T	C	6: 56,985,430	I30T	possibly damaging	Het
Vps33a	A	T	5: 123,564,984	I192N	probably damaging	Het
Vps50	A	G	6: 3,516,724	I69V	probably benign	Het
Xirp1	G	A	9: 120,018,137	T560M	probably damaging	Het
Zfp512	A	T	5: 31,471,015	T266S	possibly damaging	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
R7525:Lrch4	UTSW	5	137639465	missense	probably damaging	1.00
R7761:Lrch4	UTSW	5	137639763	missense
R7848:Lrch4	UTSW	5	137633854	missense	probably damaging	1.00
R8209:Lrch4	UTSW	5	137639735	missense
R8226:Lrch4	UTSW	5	137639735	missense
R8713:Lrch4	UTSW	5	137639863	nonsense	probably null
R9361:Lrch4	UTSW	5	137636814	missense	probably damaging	1.00
R9372:Lrch4	UTSW	5	137633691	missense	possibly damaging	0.70
R9752:Lrch4	UTSW	5	137637956	missense	probably benign
R9796:Lrch4	UTSW	5	137637007	missense	probably damaging	0.99
RF009:Lrch4	UTSW	5	137637543	critical splice acceptor site	probably null

Predicted Primers

PCR Primer
(F):5'- GAGCTGTCTTTCCGGATCTC -3'
(R):5'- ACCTGCTGCTAGATGGCTTC -3'

Sequencing Primer
(F):5'- GGGGGCCTAGACAACCTAG -3'
(R):5'- TCTCCACATCCCCTGCTACAAG -3'

Posted On

2022-06-15