Mutagenetix > Incidental Mutation

Incidental Mutation 'R8113:Lrrc4'

630996

Institutional Source

Beutler Lab

Gene Symbol

Lrrc4

Ensembl Gene

ENSMUSG00000049939

Gene Name

leucine rich repeat containing 4

Synonyms

Nag14, NGL-2, NGL2

MMRRC Submission

067542-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.208) question?

Stock #

R8113 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

28828125-28831746 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 28829902 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 148 (D148G)

Ref Sequence

ENSEMBL: ENSMUSP00000129497 (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

possibly damaging
Transcript: ENSMUST00000062304
AA Change: D571G

PolyPhen 2 Score 0.894 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000062158
Gene: ENSMUSG00000049939
AA Change: D571G

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 damaging
Transcript: ENSMUST00000171353
AA Change: D148G

PolyPhen 2 Score 0.973 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000129497
Gene: ENSMUSG00000049939
AA Change: D148G

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: 99.6%
20x: 98.7%

Validation Efficiency

96% (72/75)

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
Adcy7	T	C	8: 89,048,431 (GRCm39)	S625P	probably damaging	Het
Agpat1	T	C	17: 34,830,586 (GRCm39)	V170A	probably damaging	Het
Alg9	C	T	9: 50,720,080 (GRCm39)	Q519*	probably null	Het
Apol8	C	T	15: 77,634,336 (GRCm39)	R80H	probably benign	Het
Arhgap25	G	T	6: 87,465,287 (GRCm39)	S118*	probably null	Het
Arhgap30	T	A	1: 171,225,086 (GRCm39)	Y47*	probably null	Het
Arhgap42	C	T	9: 9,011,434 (GRCm39)	D451N	probably damaging	Het
Cabp2	T	A	19: 4,135,582 (GRCm39)	F91I	probably damaging	Het
Ccdc30	T	C	4: 119,230,943 (GRCm39)	E108G	probably benign	Het
Cfap99	T	C	5: 34,458,763 (GRCm39)	S53P	probably damaging	Het
Clec5a	C	T	6: 40,556,361 (GRCm39)	R135H	possibly damaging	Het
Cops8	T	G	1: 90,531,325 (GRCm39)	D18E	probably benign	Het
Cped1	A	T	6: 22,233,480 (GRCm39)	M779L	possibly damaging	Het
Cyp4x1	G	A	4: 114,967,263 (GRCm39)	H438Y	probably damaging	Het
Disc1	A	T	8: 125,815,014 (GRCm39)	T293S	probably benign	Het
Ercc1	T	C	7: 19,084,102 (GRCm39)	L113S	probably damaging	Het
Ermp1	G	T	19: 29,593,196 (GRCm39)	N765K	probably benign	Het
Fam83c	A	G	2: 155,676,740 (GRCm39)	I10T	probably benign	Het
Farp1	T	C	14: 121,513,008 (GRCm39)	V788A	probably benign	Het
Fbn1	C	G	2: 125,319,489 (GRCm39)	G92R	probably damaging	Het
Fsd1	T	A	17: 56,302,881 (GRCm39)	M328K	probably benign	Het
Fzd3	C	A	14: 65,440,262 (GRCm39)	S636I	probably benign	Het
Gapvd1	A	G	2: 34,594,330 (GRCm39)	S886P	probably damaging	Het
Gatad2b	T	A	3: 90,249,029 (GRCm39)	D22E	probably benign	Het
Gm7168	A	T	17: 14,169,238 (GRCm39)	K202*	probably null	Het
Gmps	T	C	3: 63,887,690 (GRCm39)	I54T	probably damaging	Het
Gp6	A	G	7: 4,397,114 (GRCm39)	I107T	probably benign	Het
Gpat2	T	C	2: 127,273,267 (GRCm39)	V217A	possibly damaging	Het
Hdlbp	T	A	1: 93,344,917 (GRCm39)	I863F	probably damaging	Het
Hmcn1	A	C	1: 150,624,841 (GRCm39)	I1021M	possibly damaging	Het
Igkv6-14	C	T	6: 70,412,087 (GRCm39)	A66T	probably benign	Het
Ippk	C	T	13: 49,599,818 (GRCm39)	P226S		Het
Iqch	A	G	9: 63,361,855 (GRCm39)	I925T	probably benign	Het
Kcnt1	A	G	2: 25,791,223 (GRCm39)	E522G	possibly damaging	Het
Kremen2	C	G	17: 23,962,776 (GRCm39)	E103D	probably damaging	Het
Lig4	G	T	8: 10,023,485 (GRCm39)	N98K	probably benign	Het
Lrrc3b	T	G	14: 15,358,232 (GRCm38)	I125L	probably benign	Het
Lrsam1	A	G	2: 32,837,901 (GRCm39)	Y218H	possibly damaging	Het
Mmrn2	G	A	14: 34,119,593 (GRCm39)	V191I	probably benign	Het
Nadk	T	A	4: 155,655,127 (GRCm39)		probably null	Het
Napb	C	A	2: 148,551,351 (GRCm39)	A61S	possibly damaging	Het
Ncan	T	A	8: 70,561,221 (GRCm39)	D582V	possibly damaging	Het
Ncl	T	C	1: 86,284,364 (GRCm39)	D244G	possibly damaging	Het
Nlrp14	A	G	7: 106,791,715 (GRCm39)	N800S	possibly damaging	Het
Nlrp9b	C	T	7: 19,753,260 (GRCm39)	T55M	probably benign	Het
Nobox	G	A	6: 43,282,951 (GRCm39)	T228I	probably benign	Het
Npffr1	C	A	10: 61,449,750 (GRCm39)	P8H	possibly damaging	Het
Nrg2	T	C	18: 36,154,156 (GRCm39)	Y587C	probably damaging	Het
Nsd1	T	G	13: 55,393,434 (GRCm39)	V448G	probably benign	Het
Or2w1	T	A	13: 21,317,371 (GRCm39)	V142D	probably benign	Het
Or5e1	G	T	7: 108,354,438 (GRCm39)	C125F	probably damaging	Het
Or8k41	T	G	2: 86,313,412 (GRCm39)	I225L	probably damaging	Het
Or9g20	A	G	2: 85,630,011 (GRCm39)	L201P	probably damaging	Het
Peg10	T	TCCC	6: 4,756,451 (GRCm39)		probably benign	Het
Ppp5c	T	C	7: 16,742,932 (GRCm39)	T229A	probably benign	Het
Pramel51	T	C	12: 88,143,850 (GRCm39)	Y329C	probably benign	Het
Prr5	C	T	15: 84,577,993 (GRCm39)	R101C	probably damaging	Het
Psg22	T	C	7: 18,456,987 (GRCm39)	M290T	probably benign	Het
Pzp	C	T	6: 128,490,694 (GRCm39)		probably null	Het
Rapgef6	T	C	11: 54,516,784 (GRCm39)	V347A	probably benign	Het
Rttn	A	T	18: 89,029,040 (GRCm39)	H586L	probably damaging	Het
Sema3f	A	T	9: 107,565,275 (GRCm39)	I259K	possibly damaging	Het
Sgpp1	A	T	12: 75,763,374 (GRCm39)	L269Q	probably damaging	Het
Slc22a8	A	C	19: 8,582,903 (GRCm39)	I195L	probably benign	Het
Slc35a5	T	C	16: 44,962,551 (GRCm39)	T425A	unknown	Het
Spata31e1	G	A	13: 49,939,548 (GRCm39)	R721C	probably benign	Het
Stard13	G	A	5: 150,986,970 (GRCm39)	T180I	probably damaging	Het
Stard9	G	A	2: 120,534,911 (GRCm39)	G3723S	probably benign	Het
Svil	A	T	18: 5,062,385 (GRCm39)	T902S	probably damaging	Het
Tnfaip8l3	T	A	9: 53,934,421 (GRCm39)	R185W	probably damaging	Het
Ttn	A	T	2: 76,590,393 (GRCm39)	D21105E	probably benign	Het
Vmn2r109	T	A	17: 20,774,729 (GRCm39)	M209L	probably benign	Het
Vmn2r125	A	G	4: 156,703,642 (GRCm39)	H340R	probably damaging	Het
Zfp946	T	C	17: 22,674,481 (GRCm39)	C412R	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
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
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'- ACAAGATGCAGACCAGCCTG -3'

Sequencing Primer
(F):5'- GAGTCATATTTGAGTTTCCTGTACC -3'
(R):5'- CCAGCCTGGATGAAGTCATG -3'

Posted On

2020-06-30