Mutagenetix > Incidental Mutation

Incidental Mutation 'R5197:Lrrc4'

400343

Institutional Source

Beutler Lab

Gene Symbol

Lrrc4

Ensembl Gene

ENSMUSG00000049939

Gene Name

leucine rich repeat containing 4

Synonyms

Nag14, NGL-2, NGL2

MMRRC Submission

042773-MU

Accession Numbers

Essential gene?

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

Stock #

R5197 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

28828125-28831746 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 28830142 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Lysine at position 68 (T68K)

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: T491K

PolyPhen 2 Score 0.716 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000062158
Gene: ENSMUSG00000049939
AA Change: T491K

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 damaging
Transcript: ENSMUST00000171353
AA Change: T68K

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

SMART Domains

Protein: ENSMUSP00000129497
Gene: ENSMUSG00000049939
AA Change: T68K

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

0.1882

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.3%
20x: 95.5%

Validation Efficiency

99% (67/68)

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: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acsbg1	T	C	9: 54,529,866 (GRCm39)	E247G	possibly damaging	Het
Adgra3	A	G	5: 50,118,096 (GRCm39)	F1151L	probably benign	Het
Afg3l2	G	T	18: 67,554,329 (GRCm39)	L458M	probably damaging	Het
Aldh4a1	A	C	4: 139,375,612 (GRCm39)		probably benign	Het
Anln	A	T	9: 22,264,077 (GRCm39)		probably null	Het
Aste1	T	C	9: 105,282,253 (GRCm39)	S74P	probably damaging	Het
Atp6v0e2	G	A	6: 48,517,051 (GRCm39)	R77H	probably benign	Het
Brpf1	A	G	6: 113,296,902 (GRCm39)	D962G	possibly damaging	Het
Btbd2	T	C	10: 80,482,253 (GRCm39)	D249G	probably damaging	Het
Catsper3	T	C	13: 55,955,989 (GRCm39)		probably null	Het
Cfap43	A	G	19: 47,885,811 (GRCm39)	L268P	probably damaging	Het
Cftr	T	C	6: 18,255,413 (GRCm39)	V540A	probably benign	Het
Col22a1	C	T	15: 71,881,255 (GRCm39)	G32D	probably damaging	Het
Col5a2	G	T	1: 45,432,241 (GRCm39)	P804Q	probably benign	Het
Cyp2d41-ps	A	G	15: 82,662,981 (GRCm39)		noncoding transcript	Het
Cyp39a1	T	G	17: 44,057,429 (GRCm39)	L423V	possibly damaging	Het
Elmo1	T	G	13: 20,748,607 (GRCm39)	V484G	probably benign	Het
Eps8	C	A	6: 137,467,288 (GRCm39)	Q656H	probably damaging	Het
Eps8	T	C	6: 137,467,289 (GRCm39)	Q656R	possibly damaging	Het
Fshb	T	C	2: 106,887,854 (GRCm39)	D55G	possibly damaging	Het
Garin1a	G	T	6: 29,281,221 (GRCm39)		probably benign	Het
H3c4	T	A	13: 23,760,304 (GRCm39)	L110Q	probably damaging	Het
Herc1	C	A	9: 66,355,786 (GRCm39)	Q2346K	probably damaging	Het
Htr3b	T	C	9: 48,856,815 (GRCm39)	D221G	probably benign	Het
Ift74	T	A	4: 94,550,833 (GRCm39)	D328E	probably benign	Het
Kif21b	A	T	1: 136,072,363 (GRCm39)	K23M	probably damaging	Het
Lgr6	C	T	1: 134,921,748 (GRCm39)	A199T	probably damaging	Het
Lipc	T	A	9: 70,705,673 (GRCm39)	E470V	probably benign	Het
Lrrc63	T	A	14: 75,322,322 (GRCm39)	H594L	possibly damaging	Het
Mfsd14a	A	T	3: 116,442,150 (GRCm39)		probably benign	Het
Mob2	T	C	7: 141,563,274 (GRCm39)		probably null	Het
Nckap5	T	A	1: 126,150,410 (GRCm39)	H105L	possibly damaging	Het
Ngef	C	A	1: 87,437,090 (GRCm39)	G133*	probably null	Het
Or14j2	T	G	17: 37,886,111 (GRCm39)	I68L	probably benign	Het
Or1e16	AGCGGTCGTAGGC	AGC	11: 73,286,480 (GRCm39)		probably null	Het
Or2t1	T	A	14: 14,328,462 (GRCm38)	M117K	probably damaging	Het
Or52s1	G	A	7: 102,861,207 (GRCm39)	V47I	probably benign	Het
Or5b120	G	T	19: 13,479,748 (GRCm39)	V14F	possibly damaging	Het
Or5g23	T	C	2: 85,438,791 (GRCm39)	I154M	probably benign	Het
Pard3	A	G	8: 127,800,040 (GRCm39)		probably null	Het
Pgm2	C	T	5: 64,263,175 (GRCm39)	A274V	possibly damaging	Het
Ppp1r9a	T	A	6: 5,156,177 (GRCm39)	S1144R	probably damaging	Het
Pramel23	A	C	4: 143,424,632 (GRCm39)	C270W	possibly damaging	Het
Prkcq	C	T	2: 11,304,227 (GRCm39)	P590L	probably damaging	Het
Psmd13	T	A	7: 140,474,374 (GRCm39)		probably null	Het
Rab3gap1	T	A	1: 127,816,931 (GRCm39)	D63E	probably benign	Het
Rag2	C	A	2: 101,461,085 (GRCm39)	T465K	probably damaging	Het
Rnase6	A	G	14: 51,367,670 (GRCm39)	M21V	unknown	Het
Rufy4	T	C	1: 74,186,822 (GRCm39)	C537R	probably damaging	Het
Ryr2	A	T	13: 11,653,316 (GRCm39)		probably null	Het
Sash1	T	G	10: 8,615,989 (GRCm39)	R624S	probably damaging	Het
Slc1a2	A	G	2: 102,586,460 (GRCm39)	I355V	probably benign	Het
Srrm2	T	C	17: 24,036,358 (GRCm39)	S1097P	probably benign	Het
Sugct	C	T	13: 17,497,861 (GRCm39)	A271T	probably damaging	Het
Tdrd7	T	C	4: 46,034,350 (GRCm39)	V1065A	probably damaging	Het
Tmprss6	T	A	15: 78,338,389 (GRCm39)	Y307F	probably damaging	Het
Tram1	T	C	1: 13,642,126 (GRCm39)	N216S	probably benign	Het
Ttk	T	C	9: 83,721,394 (GRCm39)	V93A	probably benign	Het
Ubr4	A	G	4: 139,195,408 (GRCm39)	Y1210C	probably damaging	Het
Wdr7	A	G	18: 63,871,937 (GRCm39)	K364E	probably benign	Het
Xrcc2	G	T	5: 25,897,656 (GRCm39)	H98N	probably benign	Het
Zdhhc11	A	G	13: 74,113,688 (GRCm39)	I77V	probably benign	Het
Zfp54	C	T	17: 21,654,442 (GRCm39)	S312L	probably benign	Het
Zfp647	G	A	15: 76,796,285 (GRCm39)	P125L	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
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

PCR Primer
(F):5'- GCCGCTTGCGAAGTTTATAGAAG -3'
(R):5'- AGTATACACATGCATGGTGACC -3'

Sequencing Primer
(F):5'- TTATAGAAGACAATCAACATGGCAGC -3'
(R):5'- CACATGCATGGTGACCAATGTG -3'

Posted On

2016-07-06