Mutagenetix > Incidental Mutation

Incidental Mutation 'R7660:Lrrc4'

591500

Institutional Source

Beutler Lab

Gene Symbol

Lrrc4

Ensembl Gene

ENSMUSG00000049939

Gene Name

leucine rich repeat containing 4

Synonyms

Nag14, NGL-2, NGL2

MMRRC Submission

045735-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.201) question?

Stock #

R7660 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

28828125-28831746 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 28829816 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Leucine at position 600 (I600L)

Ref Sequence

ENSEMBL: ENSMUSP00000062158 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001460] [ENSMUST00000062304] [ENSMUST00000164915] [ENSMUST00000167201] [ENSMUST00000171353]

AlphaFold

Q99PH1

Predicted Effect

probably benign
Transcript: ENSMUST00000001460

SMART Domains

Protein: ENSMUSP00000001460
Gene: ENSMUSG00000001424

Domain	Start	End	E-Value	Type
low complexity region	2	15	N/A	INTRINSIC
SNc	18	166	7.12e-54	SMART
SNc	193	328	8.37e-51	SMART
SNc	341	496	4.11e-59	SMART
SNc	525	660	3.82e-45	SMART
TUDOR	728	785	4.8e-19	SMART
Pfam:SNase	835	895	1.3e-7	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000062304
AA Change: I600L

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

SMART Domains

Protein: ENSMUSP00000062158
Gene: ENSMUSG00000049939
AA Change: I600L

Domain	Start	End	E-Value	Type
low complexity region	32	40	N/A	INTRINSIC
LRRNT	44	78	4.05e-5	SMART
LRR	72	96	1.19e2	SMART
LRR_TYP	97	120	2.24e-3	SMART
LRR	121	144	6.13e-1	SMART
LRR_TYP	145	168	5.99e-4	SMART
LRR	216	239	1.25e-1	SMART
LRR	240	263	4.71e1	SMART
LRR_TYP	264	287	2.79e-4	SMART
LRRCT	299	350	8.06e-6	SMART
IGc2	364	430	5.24e-7	SMART
low complexity region	452	462	N/A	INTRINSIC
transmembrane domain	527	549	N/A	INTRINSIC
low complexity region	575	586	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000164915

SMART Domains

Protein: ENSMUSP00000127317
Gene: ENSMUSG00000001424

Domain	Start	End	E-Value	Type
low complexity region	2	15	N/A	INTRINSIC
SNc	18	142	1.56e-18	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000167201

SMART Domains

Protein: ENSMUSP00000128737
Gene: ENSMUSG00000001424

Domain	Start	End	E-Value	Type
low complexity region	2	15	N/A	INTRINSIC
SNc	18	166	7.12e-54	SMART
SNc	193	328	8.37e-51	SMART
SNc	341	496	4.11e-59	SMART
SCOP:d1sty__	526	592	1e-4	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000171353

SMART Domains

Protein: ENSMUSP00000129497
Gene: ENSMUSG00000049939

Domain	Start	End	E-Value	Type
low complexity region	29	39	N/A	INTRINSIC
transmembrane domain	104	126	N/A	INTRINSIC
low complexity region	152	163	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.3%

Validation Efficiency

100% (70/70)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is significantly downregulated in primary brain tumors. The exact function of the protein encoded by this gene is unknown. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele exhibit hyperactivity, an absence of startle reflex, and abnormal ABR amplitude. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933427I04Rik	A	T	4: 123,754,512 (GRCm39)	H142L	possibly damaging	Het
Aadacl2fm3	A	G	3: 59,772,689 (GRCm39)	I64M	probably benign	Het
Abca13	A	G	11: 9,240,678 (GRCm39)	E847G	probably benign	Het
Abca9	T	A	11: 110,006,278 (GRCm39)	T1276S	probably benign	Het
Abcb11	C	T	2: 69,117,938 (GRCm39)		probably null	Het
Alpk1	G	C	3: 127,474,616 (GRCm39)	H462Q	probably damaging	Het
Armh1	C	A	4: 117,070,938 (GRCm39)	A396S	probably benign	Het
Atm	C	T	9: 53,356,807 (GRCm39)	V2815M	probably benign	Het
Braf	T	C	6: 39,600,575 (GRCm39)	I681V	possibly damaging	Het
Casc3	C	G	11: 98,700,699 (GRCm39)	R4G	unknown	Het
Cilk1	G	C	9: 78,074,902 (GRCm39)	V586L	probably benign	Het
Crybg1	T	C	10: 43,874,831 (GRCm39)	D759G	probably damaging	Het
Csrp2	A	G	10: 110,773,624 (GRCm39)	N103S	probably benign	Het
Faf1	A	T	4: 109,719,034 (GRCm39)	H380L	probably damaging	Het
Farp1	G	A	14: 121,514,334 (GRCm39)	A888T	probably benign	Het
Fat4	A	T	3: 39,035,309 (GRCm39)	Q2987L	probably benign	Het
Fkbp15	T	A	4: 62,232,578 (GRCm39)	T665S	probably benign	Het
Gigyf1	T	C	5: 137,519,231 (GRCm39)	S343P	probably benign	Het
Glrx3	A	G	7: 137,060,954 (GRCm39)	Y196C	probably damaging	Het
Gm3278	T	G	14: 16,080,387 (GRCm39)	L66R	probably damaging	Het
Ifi205	A	G	1: 173,855,814 (GRCm39)	V72A	probably benign	Het
Ift140	T	G	17: 25,270,798 (GRCm39)	L708R	probably damaging	Het
Ints13	A	T	6: 146,458,836 (GRCm39)	L328M	probably benign	Het
Itfg2	A	G	6: 128,401,709 (GRCm39)	I23T	probably damaging	Het
Ldha	C	T	7: 46,499,681 (GRCm39)	P100S	unknown	Het
Lmtk2	T	A	5: 144,085,158 (GRCm39)	L210H	probably damaging	Het
Map2	C	A	1: 66,453,536 (GRCm39)	P809T	probably damaging	Het
Matn2	T	A	15: 34,423,874 (GRCm39)	C577*	probably null	Het
Matn2	A	G	15: 34,403,092 (GRCm39)	K439R	probably benign	Het
Mep1a	C	T	17: 43,789,868 (GRCm39)	G494S	probably benign	Het
Mtmr4	T	C	11: 87,495,406 (GRCm39)	F488L	probably damaging	Het
Mtus1	G	T	8: 41,469,248 (GRCm39)	T8K	probably benign	Het
Mug1	C	A	6: 121,838,179 (GRCm39)	H470N	possibly damaging	Het
Mybpc1	T	C	10: 88,384,716 (GRCm39)	T523A	possibly damaging	Het
Ncoa3	C	T	2: 165,911,241 (GRCm39)	P1334S	probably benign	Het
Neb	T	G	2: 52,139,451 (GRCm39)	M119L		Het
Nox4	T	C	7: 87,019,230 (GRCm39)	Y408H	probably damaging	Het
Nxpe3	C	T	16: 55,664,690 (GRCm39)	R510Q	probably damaging	Het
Or4c58	T	C	2: 89,674,787 (GRCm39)	T177A	probably benign	Het
Or4f52	C	T	2: 111,061,960 (GRCm39)	M59I	probably damaging	Het
Or5p60	A	G	7: 107,724,041 (GRCm39)	V143A	probably benign	Het
Or6c214	C	A	10: 129,590,432 (GRCm39)	E296*	probably null	Het
Or7g23	T	C	9: 19,086,804 (GRCm39)	H56R	probably benign	Het
Or8k31-ps1	A	T	2: 86,356,174 (GRCm39)	S116T	possibly damaging	Het
Paip1	C	T	13: 119,587,306 (GRCm39)	T390I	possibly damaging	Het
Pax8	T	C	2: 24,326,573 (GRCm39)	Y263C	probably benign	Het
Pcdha11	T	A	18: 37,138,904 (GRCm39)	Y178N	probably benign	Het
Pcdhga11	C	T	18: 37,890,183 (GRCm39)	T397M	possibly damaging	Het
Pdlim5	G	T	3: 141,964,946 (GRCm39)	H428N	probably damaging	Het
Pigg	G	A	5: 108,486,485 (GRCm39)	V713I	probably benign	Het
Rgs3	A	G	4: 62,619,349 (GRCm39)	D478G	possibly damaging	Het
Scgb2b11	C	T	7: 31,909,883 (GRCm39)	E68K	probably damaging	Het
Sema4b	C	A	7: 79,869,995 (GRCm39)	Q428K	probably benign	Het
Semp2l2a	A	T	8: 13,887,995 (GRCm39)	I32K	probably benign	Het
Serpine2	T	C	1: 79,780,622 (GRCm39)	T276A	probably benign	Het
Sgo2b	G	A	8: 64,393,108 (GRCm39)	H110Y	probably benign	Het
Slc12a7	T	C	13: 73,954,208 (GRCm39)	L833S	probably benign	Het
Slc6a15	T	A	10: 103,229,241 (GRCm39)		probably null	Het
Srfbp1	G	A	18: 52,608,671 (GRCm39)	V24I	probably damaging	Het
Stpg2	A	T	3: 139,407,458 (GRCm39)	N537Y	probably damaging	Het
Svep1	A	T	4: 58,087,782 (GRCm39)	S1766T	probably benign	Het
Tiam2	T	A	17: 3,532,880 (GRCm39)	M1K	probably null	Het
Tmem245	A	T	4: 56,899,170 (GRCm39)	I661K	possibly damaging	Het
Trim5	T	C	7: 103,928,569 (GRCm39)	H124R	probably damaging	Het
Trim67	T	A	8: 125,547,024 (GRCm39)	L478Q	probably damaging	Het
Triml2	A	G	8: 43,646,357 (GRCm39)	D282G	probably damaging	Het
Txndc11	T	C	16: 10,905,793 (GRCm39)	Y579C	probably damaging	Het
Ube3c	T	A	5: 29,824,629 (GRCm39)	D551E	probably damaging	Het
Vmn1r194	T	C	13: 22,428,767 (GRCm39)	V128A	not run	Het
Vmn2r130	T	A	17: 23,296,006 (GRCm39)	D725E	probably damaging	Het
Vmn2r70	T	G	7: 85,218,130 (GRCm39)	N56T	probably damaging	Het
Wdr95	T	C	5: 149,517,945 (GRCm39)	V501A	possibly damaging	Het
Zc3h8	T	C	2: 128,772,742 (GRCm39)	T249A	probably damaging	Het
Zfp54	T	C	17: 21,654,501 (GRCm39)	C332R	probably damaging	Het

Other mutations in Lrrc4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02230:Lrrc4	APN	6	28,830,879 (GRCm39)	missense	probably damaging	0.99
IGL03223:Lrrc4	APN	6	28,831,469 (GRCm39)	missense	probably damaging	1.00
IGL03410:Lrrc4	APN	6	28,830,515 (GRCm39)	missense	probably damaging	1.00
R0233:Lrrc4	UTSW	6	28,829,734 (GRCm39)	missense	probably benign	0.05
R0233:Lrrc4	UTSW	6	28,829,734 (GRCm39)	missense	probably benign	0.05
R0456:Lrrc4	UTSW	6	28,831,103 (GRCm39)	missense	probably damaging	1.00
R1162:Lrrc4	UTSW	6	28,831,083 (GRCm39)	missense	probably damaging	1.00
R2001:Lrrc4	UTSW	6	28,830,904 (GRCm39)	missense	probably damaging	1.00
R2089:Lrrc4	UTSW	6	28,830,586 (GRCm39)	missense	probably benign	0.45
R2091:Lrrc4	UTSW	6	28,830,586 (GRCm39)	missense	probably benign	0.45
R2091:Lrrc4	UTSW	6	28,830,586 (GRCm39)	missense	probably benign	0.45
R2353:Lrrc4	UTSW	6	28,831,451 (GRCm39)	missense	probably benign	0.00
R5079:Lrrc4	UTSW	6	28,830,769 (GRCm39)	missense	possibly damaging	0.69
R5197:Lrrc4	UTSW	6	28,830,142 (GRCm39)	missense	probably damaging	1.00
R6701:Lrrc4	UTSW	6	28,830,905 (GRCm39)	missense	possibly damaging	0.95
R6755:Lrrc4	UTSW	6	28,831,292 (GRCm39)	missense	probably damaging	1.00
R7661:Lrrc4	UTSW	6	28,829,762 (GRCm39)	missense	probably benign	0.00
R8113:Lrrc4	UTSW	6	28,829,902 (GRCm39)	missense	probably damaging	0.97
R8272:Lrrc4	UTSW	6	28,662,192 (GRCm39)	missense	unknown
R9074:Lrrc4	UTSW	6	28,831,595 (GRCm39)	missense	probably damaging	0.99
R9094:Lrrc4	UTSW	6	28,830,206 (GRCm39)	missense	possibly damaging	0.92
R9197:Lrrc4	UTSW	6	28,831,318 (GRCm39)	missense	probably benign	0.01
R9447:Lrrc4	UTSW	6	28,830,650 (GRCm39)	missense	probably benign	0.08
R9803:Lrrc4	UTSW	6	28,662,199 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- CCCCACTCTGTACAAAAGTTGC -3'
(R):5'- AGCTGCTGCCATGTTGATTG -3'

Sequencing Primer
(F):5'- ATAAGTTTTTGAGGGAGGGGGAGTC -3'
(R):5'- GTCTTCTATAAACTTCGCAAGCGG -3'

Posted On

2019-11-12