Mutagenetix > Incidental Mutation

Incidental Mutation 'R6701:Lrrc4'

528738

Institutional Source

Beutler Lab

Gene Symbol

Lrrc4

Ensembl Gene

ENSMUSG00000049939

Gene Name

leucine rich repeat containing 4

Synonyms

Nag14, NGL-2, NGL2

MMRRC Submission

044819-MU

Accession Numbers

Essential gene?

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

Stock #

R6701 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

28828125-28831746 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 28830905 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 237 (F237L)

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

possibly damaging
Transcript: ENSMUST00000062304
AA Change: F237L

PolyPhen 2 Score 0.953 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000062158
Gene: ENSMUSG00000049939
AA Change: F237L

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

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.4%
20x: 96.0%

Validation Efficiency

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Akap12	A	T	10: 4,305,243 (GRCm39)	K684N	probably damaging	Het
Akna	C	T	4: 63,313,517 (GRCm39)	G202D	probably benign	Het
Alpk1	T	A	3: 127,522,985 (GRCm39)	D19V	probably damaging	Het
Arid4a	A	T	12: 71,134,286 (GRCm39)	K1196I	probably damaging	Het
Asic3	A	T	5: 24,619,127 (GRCm39)	M140L	possibly damaging	Het
Bfsp2	C	T	9: 103,357,077 (GRCm39)	V117M	possibly damaging	Het
Bltp3a	T	A	17: 28,106,331 (GRCm39)	C952*	probably null	Het
Cd244a	C	A	1: 171,401,723 (GRCm39)	L150M	possibly damaging	Het
Cd3e	T	C	9: 44,912,351 (GRCm39)	Y131C	probably damaging	Het
Clptm1l	T	C	13: 73,757,025 (GRCm39)	I202T	probably benign	Het
Cnot4	G	T	6: 35,045,539 (GRCm39)	T224K	probably damaging	Het
Col24a1	A	G	3: 145,020,141 (GRCm39)	T171A	probably benign	Het
Col6a3	C	T	1: 90,720,184 (GRCm39)	R1552Q	probably benign	Het
Dcc	T	A	18: 71,942,191 (GRCm39)	T309S	probably benign	Het
Ddx21	T	C	10: 62,426,470 (GRCm39)	Y461C	probably damaging	Het
Dnah10	G	A	5: 124,837,223 (GRCm39)	V989M	probably benign	Het
Dppa4	A	T	16: 48,111,674 (GRCm39)	K220*	probably null	Het
Dysf	G	A	6: 84,089,172 (GRCm39)	G912S	probably damaging	Het
Efhb	A	T	17: 53,706,091 (GRCm39)	N815K	probably benign	Het
Eml6	T	A	11: 29,735,748 (GRCm39)	L1139F	probably damaging	Het
Eprs1	T	G	1: 185,103,087 (GRCm39)	I78S	probably damaging	Het
Fat1	C	A	8: 45,403,718 (GRCm39)	S156R	probably damaging	Het
Firrm	T	C	1: 163,799,412 (GRCm39)		probably null	Het
Frzb	G	A	2: 80,277,163 (GRCm39)	R8W	possibly damaging	Het
Guf1	T	A	5: 69,715,596 (GRCm39)	D47E	probably damaging	Het
Haus3	A	T	5: 34,325,078 (GRCm39)	F194I	probably damaging	Het
Hivep3	C	T	4: 119,951,737 (GRCm39)	R18W	probably damaging	Het
Hnf1b	A	G	11: 83,779,920 (GRCm39)	T392A	probably damaging	Het
Hsd17b1	C	A	11: 100,970,981 (GRCm39)	C312*	probably null	Het
Ighg2b	T	C	12: 113,270,699 (GRCm39)	T144A	unknown	Het
Iqub	T	A	6: 24,449,744 (GRCm39)	N707I	probably damaging	Het
Irag2	G	T	6: 145,090,702 (GRCm39)	E61*	probably null	Het
Jhy	T	C	9: 40,828,887 (GRCm39)	R340G	probably damaging	Het
Klra3	C	G	6: 130,307,216 (GRCm39)	V144L	probably benign	Het
Lamp5	C	G	2: 135,901,483 (GRCm39)	N102K	possibly damaging	Het
Lyst	T	A	13: 13,856,070 (GRCm39)	C2464S	probably benign	Het
Maml1	T	C	11: 50,157,509 (GRCm39)	E222G	probably damaging	Het
Med15	C	T	16: 17,489,447 (GRCm39)		probably benign	Het
Naalad2	T	C	9: 18,296,444 (GRCm39)	I69V	probably null	Het
Neb	T	C	2: 52,181,220 (GRCm39)	K1129R	probably damaging	Het
Nsun6	A	T	2: 15,041,113 (GRCm39)	N159K	probably benign	Het
Nup153	A	T	13: 46,840,541 (GRCm39)	N1022K	probably benign	Het
Or1e29	T	C	11: 73,667,296 (GRCm39)	N286D	probably damaging	Het
Or5g9	A	G	2: 85,552,675 (GRCm39)	K309E	probably benign	Het
Or5w15	C	T	2: 87,567,753 (GRCm39)	R305K	probably benign	Het
Otof	T	A	5: 30,528,141 (GRCm39)	K1901*	probably null	Het
Pde1c	A	T	6: 56,158,685 (GRCm39)	Y136N	probably damaging	Het
Phc1	G	T	6: 122,302,733 (GRCm39)	N263K	probably damaging	Het
Plxna1	A	T	6: 89,296,430 (GRCm39)	D1871E	probably damaging	Het
Prdm6	T	A	18: 53,669,751 (GRCm39)	M123K	possibly damaging	Het
Ranbp17	T	C	11: 33,425,066 (GRCm39)	D430G	probably damaging	Het
Rsl24d1	C	A	9: 73,022,279 (GRCm39)	T287K	probably damaging	Het
Scn1a	G	A	2: 66,168,304 (GRCm39)	R101W	probably damaging	Het
Scn8a	A	G	15: 100,937,977 (GRCm39)	D1741G	probably damaging	Het
Serpinb1c	T	C	13: 33,080,924 (GRCm39)	Q53R	probably benign	Het
Serpinf2	C	T	11: 75,323,269 (GRCm39)	R479H	probably damaging	Het
Sis	T	A	3: 72,856,860 (GRCm39)	D448V	probably damaging	Het
Slc27a6	T	A	18: 58,712,947 (GRCm39)	D256E	probably benign	Het
Slc30a8	A	G	15: 52,194,970 (GRCm39)	Y243C	possibly damaging	Het
Slc35f5	T	C	1: 125,490,347 (GRCm39)	V103A	probably damaging	Het
Slc44a2	T	C	9: 21,232,149 (GRCm39)		probably null	Het
Slc7a9	T	C	7: 35,159,274 (GRCm39)	L327P	probably damaging	Het
Stat4	A	G	1: 52,142,133 (GRCm39)	Y660C	probably damaging	Het
Terb1	T	C	8: 105,199,388 (GRCm39)	T519A	possibly damaging	Het
Tonsl	A	T	15: 76,513,500 (GRCm39)	S1245T	probably damaging	Het
Ttn	A	T	2: 76,619,162 (GRCm39)	S16072R	probably damaging	Het
Ttn	A	T	2: 76,739,590 (GRCm39)	Y3650N	probably benign	Het
Uso1	T	C	5: 92,314,444 (GRCm39)	F117S	probably damaging	Het
Vmn1r211	T	C	13: 23,035,779 (GRCm39)	H296R	probably benign	Het
Vmn2r67	G	A	7: 84,802,023 (GRCm39)	P93S	probably damaging	Het
Xirp2	A	T	2: 67,346,569 (GRCm39)	I2937F	possibly damaging	Het
Zc2hc1c	C	A	12: 85,336,446 (GRCm39)		probably null	Het
Zfp12	T	C	5: 143,230,219 (GRCm39)	V182A	probably benign	Het
Zfp473	G	T	7: 44,382,218 (GRCm39)	A705D	possibly damaging	Het
Zfp937	G	T	2: 150,081,136 (GRCm39)	G389C	probably damaging	Het
Zfp990	A	G	4: 145,264,748 (GRCm39)	D582G	probably benign	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
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

PCR Primer
(F):5'- GTGCAACTCCACCAGGTATCTC -3'
(R):5'- TTCTTATGCCTTCAACCGGG -3'

Sequencing Primer
(F):5'- ACCAGGTATCTCAGGGGTG -3'
(R):5'- CCTCATGCGTCTGGACTTGG -3'

Posted On

2018-07-24