Mutagenetix > Incidental Mutation

Incidental Mutation 'R1162:Lrrc4'

100462

Institutional Source

Beutler Lab

Gene Symbol

Lrrc4

Ensembl Gene

ENSMUSG00000049939

Gene Name

leucine rich repeat containing 4

Synonyms

Nag14, NGL-2, NGL2

MMRRC Submission

039235-MU

Accession Numbers

Essential gene?

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

Stock #

R1162 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

28828125-28831746 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 28831083 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Phenylalanine at position 177 (L177F)

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 damaging
Transcript: ENSMUST00000062304
AA Change: L177F

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

SMART Domains

Protein: ENSMUSP00000062158
Gene: ENSMUSG00000049939
AA Change: L177F

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

noncoding transcript
Transcript: ENSMUST00000169579

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000171195

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

Meta Mutation Damage Score

0.2032

Coding Region Coverage

1x: 99.1%
3x: 98.2%
10x: 96.0%
20x: 91.9%

Validation Efficiency

98% (55/56)

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: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9430015G10Rik	T	C	4: 156,206,875 (GRCm39)		probably null	Het
Adamts12	T	A	15: 11,277,544 (GRCm39)		probably null	Het
Ccn3	T	A	15: 54,611,178 (GRCm39)	C104*	probably null	Het
Cops4	T	C	5: 100,678,023 (GRCm39)		probably benign	Het
Cul7	T	A	17: 46,974,116 (GRCm39)	L1467H	probably damaging	Het
Dgkh	A	G	14: 78,861,891 (GRCm39)	C125R	probably damaging	Het
Dgkz	A	T	2: 91,774,789 (GRCm39)	I65N	probably damaging	Het
Dock10	T	A	1: 80,546,559 (GRCm39)	H743L	possibly damaging	Het
Dscaml1	T	C	9: 45,663,647 (GRCm39)		probably benign	Het
Flt4	C	T	11: 49,527,166 (GRCm39)		probably benign	Het
Gbe1	A	T	16: 70,178,738 (GRCm39)		probably benign	Het
Gm7275	A	G	16: 47,894,395 (GRCm39)		noncoding transcript	Het
Gpatch1	A	G	7: 35,002,905 (GRCm39)		probably benign	Het
Gpr137c	A	G	14: 45,481,615 (GRCm39)	I144V	possibly damaging	Het
Igsf9b	T	C	9: 27,238,185 (GRCm39)	S563P	probably benign	Het
Insl5	C	T	4: 102,875,438 (GRCm39)	R104Q	probably benign	Het
Kcnj2	T	A	11: 110,963,793 (GRCm39)	V395D	probably benign	Het
Ksr2	A	G	5: 117,693,020 (GRCm39)		probably benign	Het
Mapkbp1	A	G	2: 119,855,799 (GRCm39)	E1506G	possibly damaging	Het
Morc3	A	C	16: 93,649,996 (GRCm39)	Y259S	probably damaging	Het
Mrpl43	T	G	19: 44,994,797 (GRCm39)	S13R	possibly damaging	Het
Myh4	A	G	11: 67,149,439 (GRCm39)	N1724D	probably damaging	Het
Nab1	A	G	1: 52,529,186 (GRCm39)	M237T	probably damaging	Het
Nav2	A	G	7: 49,185,788 (GRCm39)		probably benign	Het
Nfix	G	A	8: 85,453,155 (GRCm39)	R300C	probably damaging	Het
Nup155	A	T	15: 8,187,244 (GRCm39)	H1391L	probably damaging	Het
Or2h15	A	T	17: 38,441,984 (GRCm39)	V33D	possibly damaging	Het
Or5ac15	T	C	16: 58,939,735 (GRCm39)	R233G	probably damaging	Het
Or5p80	A	G	7: 108,230,120 (GRCm39)	N307S	probably benign	Het
Phf2	A	T	13: 48,973,117 (GRCm39)		probably benign	Het
Ppef2	A	C	5: 92,400,980 (GRCm39)	F13L	probably benign	Het
Pwwp4a	G	T	X: 72,171,261 (GRCm39)	G218C	probably damaging	Het
Sap130	C	T	18: 31,781,226 (GRCm39)	P130S	probably damaging	Het
Scn11a	A	G	9: 119,634,710 (GRCm39)		probably benign	Het
Sec31b	C	A	19: 44,506,087 (GRCm39)	E940*	probably null	Het
Sgce	A	G	6: 4,691,419 (GRCm39)		probably benign	Het
Sh3glb2	A	T	2: 30,240,600 (GRCm39)	I155N	probably damaging	Het
Sirt2	A	T	7: 28,485,247 (GRCm39)	D218V	probably damaging	Het
Slc16a10	T	C	10: 39,952,549 (GRCm39)	H315R	probably benign	Het
Sox5	A	G	6: 143,906,538 (GRCm39)	Y306H	probably damaging	Het
Sucla2	C	T	14: 73,798,074 (GRCm39)		probably benign	Het
Tab2	A	G	10: 7,800,483 (GRCm39)	V23A	probably damaging	Het
Trak1	G	T	9: 121,282,407 (GRCm39)	V429F	possibly damaging	Het
Trat1	T	C	16: 48,560,572 (GRCm39)	S102G	possibly damaging	Het
Trub1	G	A	19: 57,461,191 (GRCm39)	V156I	probably benign	Het
Tspan32	T	A	7: 142,560,735 (GRCm39)	M61K	probably damaging	Het
Unc13a	T	A	8: 72,100,561 (GRCm39)	T1076S	probably benign	Het
Vangl2	A	G	1: 171,832,414 (GRCm39)	Y481H	probably damaging	Het
Vmn2r105	C	T	17: 20,447,973 (GRCm39)	E284K	probably benign	Het
Vmn2r60	A	T	7: 41,845,195 (GRCm39)	I853F	probably benign	Het
Yrdc	T	C	4: 124,748,254 (GRCm39)		probably benign	Het
Zfp595	A	T	13: 67,465,259 (GRCm39)	C335S	probably damaging	Het
Zfp872	A	G	9: 22,110,910 (GRCm39)	S149G	possibly 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
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
R7660:Lrrc4	UTSW	6	28,829,816 (GRCm39)	missense	probably benign	0.00
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

Posted On

2014-01-15