Mutagenetix > Incidental Mutation

Incidental Mutation 'R0315:Lrrc9'

25414

Institutional Source

Beutler Lab

Gene Symbol

Lrrc9

Ensembl Gene

ENSMUSG00000021090

Gene Name

leucine rich repeat containing 9

Synonyms

4921529O18Rik, 4930432K16Rik

MMRRC Submission

038525-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.209) question?

Stock #

R0315 (G1)

Quality Score

211

Status

Validated

Chromosome

Chromosomal Location

72481391-72561269 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 72502802 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 258 (T258A)

Ref Sequence

ENSEMBL: ENSMUSP00000152125 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000161284] [ENSMUST00000162159] [ENSMUST00000221360]

AlphaFold

Q8CDN9

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160394

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161195

Predicted Effect

probably benign
Transcript: ENSMUST00000161284
AA Change: T258A

PolyPhen 2 Score 0.420 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000124602
Gene: ENSMUSG00000021090
AA Change: T258A

Domain	Start	End	E-Value	Type
Pfam:LRR_4	77	118	2.8e-11	PFAM
LRR	119	140	8.49e1	SMART
LRR	141	164	2.27e1	SMART
LRR	165	187	2.09e2	SMART
LRRcap	210	228	6.12e1	SMART
low complexity region	373	384	N/A	INTRINSIC
low complexity region	424	436	N/A	INTRINSIC
LRR	706	727	1.41e2	SMART
LRR	728	749	6.78e1	SMART
LRR	750	773	7.17e1	SMART
LRRcap	793	811	2.26e2	SMART
LRR	943	966	2.67e-1	SMART
LRR	967	992	1.22e1	SMART
LRRcap	1031	1049	4.37e0	SMART
low complexity region	1109	1120	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161957

Predicted Effect

probably damaging
Transcript: ENSMUST00000162159
AA Change: T258A

PolyPhen 2 Score 0.960 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000124394
Gene: ENSMUSG00000021090
AA Change: T258A

Domain	Start	End	E-Value	Type
LRR	53	74	5.39e2	SMART
LRR	75	96	1.14e2	SMART
LRR	97	118	7.9e-4	SMART
LRR	119	140	2.75e-3	SMART
LRR	141	164	2.27e1	SMART
LRR	164	185	1.87e1	SMART
LRRcap	210	228	6.12e1	SMART
low complexity region	373	384	N/A	INTRINSIC
low complexity region	424	436	N/A	INTRINSIC
LRR	705	726	1.41e2	SMART
LRR	727	748	6.78e1	SMART
LRR	749	771	1.37e1	SMART
LRRcap	792	810	2.26e2	SMART
LRR	898	919	2.62e1	SMART
LRR	920	941	5.17e1	SMART
LRR	942	965	2.67e-1	SMART
LRR	966	991	1.22e1	SMART
LRR	1013	1032	4.42e2	SMART
LRRcap	1030	1048	4.37e0	SMART
low complexity region	1108	1119	N/A	INTRINSIC
LRR	1128	1150	2.4e1	SMART
LRR	1191	1209	5.7e2	SMART
LRR	1215	1236	1.03e-2	SMART
LRR	1237	1260	8.48e0	SMART
LRR	1283	1304	2.67e-1	SMART
Blast:LRR	1308	1333	4e-6	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162179

Predicted Effect

probably damaging
Transcript: ENSMUST00000221360
AA Change: T258A

PolyPhen 2 Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)

Meta Mutation Damage Score

0.0848

Coding Region Coverage

1x: 98.9%
3x: 97.8%
10x: 94.9%
20x: 88.9%

Validation Efficiency

100% (42/42)

Allele List at MGI

Other mutations in this stock

Total: 42 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aars2	G	A	17: 45,826,378 (GRCm39)	R409Q	possibly damaging	Het
Ank3	A	T	10: 69,838,347 (GRCm39)	Q825L	probably damaging	Het
Ap1g1	A	G	8: 110,545,667 (GRCm39)	I107V	probably benign	Het
Bub1b	A	T	2: 118,457,457 (GRCm39)		probably benign	Het
Cd86	C	T	16: 36,441,306 (GRCm39)	V54I	possibly damaging	Het
Dpys	T	G	15: 39,720,734 (GRCm39)	I9L	probably benign	Het
Fbxl17	G	A	17: 63,663,846 (GRCm39)	R67C	probably damaging	Het
Flg2	G	T	3: 93,122,029 (GRCm39)	G1400C	unknown	Het
Gm28042	T	C	2: 119,869,538 (GRCm39)	L634P	probably damaging	Het
Gm6712	G	A	17: 17,536,380 (GRCm39)		noncoding transcript	Het
Gpbp1	T	G	13: 111,573,072 (GRCm39)	E360A	possibly damaging	Het
Hmgn1	A	C	16: 95,926,017 (GRCm39)	I52R	probably benign	Het
Ing2	A	C	8: 48,122,125 (GRCm39)	M141R	probably benign	Het
Klhl2	A	T	8: 65,196,053 (GRCm39)	Y563*	probably null	Het
Map1b	A	T	13: 99,567,624 (GRCm39)	I1699N	unknown	Het
Map2k5	A	T	9: 63,210,433 (GRCm39)	H185Q	probably damaging	Het
Mpv17l	A	T	16: 13,758,863 (GRCm39)	I96L	probably benign	Het
Mroh1	C	T	15: 76,311,800 (GRCm39)	A511V	possibly damaging	Het
Nop53	T	C	7: 15,679,235 (GRCm39)	D90G	probably damaging	Het
Or10k2	T	C	8: 84,268,001 (GRCm39)	V76A	possibly damaging	Het
Or5b97	A	T	19: 12,878,598 (GRCm39)	V182D	possibly damaging	Het
Or5w20	A	T	2: 87,727,410 (GRCm39)	Y289F	probably damaging	Het
Or6c209	T	A	10: 129,483,366 (GRCm39)	I123N	probably damaging	Het
Pkd2	T	A	5: 104,607,716 (GRCm39)	S72T	possibly damaging	Het
Prc1	T	C	7: 79,963,284 (GRCm39)	S587P	probably damaging	Het
Rdh7	G	T	10: 127,724,265 (GRCm39)	T73K	possibly damaging	Het
Runx1	T	C	16: 92,402,655 (GRCm39)	N429S	probably damaging	Het
Skint7	G	A	4: 111,845,315 (GRCm39)	A376T	possibly damaging	Het
Slc16a14	T	C	1: 84,890,217 (GRCm39)	I363V	possibly damaging	Het
Smarcal1	C	T	1: 72,634,970 (GRCm39)	Q350*	probably null	Het
Soat1	T	A	1: 156,268,083 (GRCm39)	K275*	probably null	Het
Speg	T	C	1: 75,391,780 (GRCm39)	V1571A	possibly damaging	Het
Stat5b	G	C	11: 100,679,286 (GRCm39)	D605E	probably benign	Het
Susd4	G	A	1: 182,686,077 (GRCm39)	R209H	probably benign	Het
Tlr1	T	G	5: 65,084,271 (GRCm39)	D102A	probably damaging	Het
Tm4sf5	A	G	11: 70,401,462 (GRCm39)	N154D	probably damaging	Het
Tmigd3	T	A	3: 105,824,085 (GRCm39)	M18K	probably damaging	Het
Ube2h	A	T	6: 30,241,412 (GRCm39)	V86E	probably damaging	Het
Utp20	A	G	10: 88,643,283 (GRCm39)	L613P	probably damaging	Het
Vmn2r117	G	A	17: 23,679,139 (GRCm39)	S695L	probably benign	Het
Washc5	T	C	15: 59,213,825 (GRCm39)	D427G	probably damaging	Het
Zfp462	T	A	4: 55,079,314 (GRCm39)	F2403I	probably damaging	Het

Other mutations in Lrrc9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00092:Lrrc9	APN	12	72,533,017 (GRCm39)	missense	possibly damaging	0.63
IGL00843:Lrrc9	APN	12	72,510,191 (GRCm39)	missense	possibly damaging	0.78
IGL01923:Lrrc9	APN	12	72,557,186 (GRCm39)	missense	possibly damaging	0.93
IGL02027:Lrrc9	APN	12	72,517,108 (GRCm39)	splice site	probably benign
IGL02271:Lrrc9	APN	12	72,557,155 (GRCm39)	missense	probably benign	0.06
IGL02398:Lrrc9	APN	12	72,513,677 (GRCm39)	missense	probably benign
IGL02795:Lrrc9	APN	12	72,525,542 (GRCm39)	missense	probably damaging	1.00
IGL02931:Lrrc9	APN	12	72,500,923 (GRCm39)	missense	probably damaging	1.00
IGL03257:Lrrc9	APN	12	72,496,542 (GRCm39)	missense	probably benign
BB006:Lrrc9	UTSW	12	72,533,071 (GRCm39)	missense	possibly damaging	0.92
BB016:Lrrc9	UTSW	12	72,533,071 (GRCm39)	missense	possibly damaging	0.92
IGL02799:Lrrc9	UTSW	12	72,553,178 (GRCm39)	missense	probably damaging	1.00
R0172:Lrrc9	UTSW	12	72,510,260 (GRCm39)	missense	possibly damaging	0.50
R0492:Lrrc9	UTSW	12	72,525,537 (GRCm39)	missense	possibly damaging	0.47
R0617:Lrrc9	UTSW	12	72,529,788 (GRCm39)	missense	probably damaging	1.00
R0639:Lrrc9	UTSW	12	72,533,062 (GRCm39)	missense	probably damaging	1.00
R0987:Lrrc9	UTSW	12	72,557,156 (GRCm39)	missense	probably benign	0.00
R1325:Lrrc9	UTSW	12	72,543,878 (GRCm39)	missense	probably damaging	0.99
R1465:Lrrc9	UTSW	12	72,547,533 (GRCm39)	missense	probably benign	0.05
R1465:Lrrc9	UTSW	12	72,547,533 (GRCm39)	missense	probably benign	0.05
R1479:Lrrc9	UTSW	12	72,507,599 (GRCm39)	nonsense	probably null
R1564:Lrrc9	UTSW	12	72,533,827 (GRCm39)	missense	probably damaging	1.00
R1626:Lrrc9	UTSW	12	72,542,435 (GRCm39)	splice site	probably null
R1632:Lrrc9	UTSW	12	72,506,794 (GRCm39)	splice site	probably null
R1715:Lrrc9	UTSW	12	72,524,073 (GRCm39)	missense	probably damaging	1.00
R1743:Lrrc9	UTSW	12	72,502,891 (GRCm39)	missense	probably damaging	1.00
R1779:Lrrc9	UTSW	12	72,502,772 (GRCm39)	nonsense	probably null
R1866:Lrrc9	UTSW	12	72,543,912 (GRCm39)	missense	probably damaging	0.97
R1878:Lrrc9	UTSW	12	72,522,938 (GRCm39)	critical splice donor site	probably null
R1990:Lrrc9	UTSW	12	72,544,635 (GRCm39)	missense	probably damaging	0.99
R2361:Lrrc9	UTSW	12	72,510,244 (GRCm39)	missense	possibly damaging	0.52
R3752:Lrrc9	UTSW	12	72,507,580 (GRCm39)	nonsense	probably null
R3833:Lrrc9	UTSW	12	72,529,765 (GRCm39)	missense	probably damaging	1.00
R4134:Lrrc9	UTSW	12	72,513,740 (GRCm39)	missense	probably benign	0.00
R4651:Lrrc9	UTSW	12	72,524,160 (GRCm39)	missense	probably damaging	1.00
R4652:Lrrc9	UTSW	12	72,524,160 (GRCm39)	missense	probably damaging	1.00
R4659:Lrrc9	UTSW	12	72,517,038 (GRCm39)	missense	probably damaging	1.00
R4831:Lrrc9	UTSW	12	72,546,453 (GRCm39)	missense	probably damaging	1.00
R4857:Lrrc9	UTSW	12	72,546,466 (GRCm39)	missense	possibly damaging	0.94
R5017:Lrrc9	UTSW	12	72,553,099 (GRCm39)	missense	possibly damaging	0.86
R5163:Lrrc9	UTSW	12	72,496,163 (GRCm39)	missense	probably damaging	1.00
R5279:Lrrc9	UTSW	12	72,542,368 (GRCm39)	missense	possibly damaging	0.80
R5434:Lrrc9	UTSW	12	72,500,862 (GRCm39)	missense	probably damaging	0.98
R5783:Lrrc9	UTSW	12	72,502,827 (GRCm39)	missense	possibly damaging	0.62
R6021:Lrrc9	UTSW	12	72,516,005 (GRCm39)	missense	probably damaging	0.97
R6214:Lrrc9	UTSW	12	72,506,627 (GRCm39)	missense	probably damaging	1.00
R6255:Lrrc9	UTSW	12	72,533,797 (GRCm39)	missense	probably benign	0.33
R6538:Lrrc9	UTSW	12	72,547,703 (GRCm39)	missense	probably benign	0.08
R6563:Lrrc9	UTSW	12	72,533,169 (GRCm39)	splice site	probably null
R6672:Lrrc9	UTSW	12	72,520,710 (GRCm39)	missense	possibly damaging	0.88
R6919:Lrrc9	UTSW	12	72,553,167 (GRCm39)	missense	probably benign	0.01
R6929:Lrrc9	UTSW	12	72,497,546 (GRCm39)	missense	probably benign	0.41
R7092:Lrrc9	UTSW	12	72,510,238 (GRCm39)	missense	possibly damaging	0.81
R7150:Lrrc9	UTSW	12	72,513,726 (GRCm39)	missense	probably benign	0.00
R7338:Lrrc9	UTSW	12	72,510,305 (GRCm39)	splice site	probably null
R7398:Lrrc9	UTSW	12	72,547,590 (GRCm39)	missense	probably damaging	0.98
R7477:Lrrc9	UTSW	12	72,550,301 (GRCm39)	critical splice donor site	probably null
R7501:Lrrc9	UTSW	12	72,496,490 (GRCm39)	missense	probably damaging	1.00
R7542:Lrrc9	UTSW	12	72,553,094 (GRCm39)	missense	probably damaging	0.96
R7816:Lrrc9	UTSW	12	72,542,466 (GRCm39)	missense	probably damaging	1.00
R7870:Lrrc9	UTSW	12	72,532,964 (GRCm39)	missense	probably damaging	0.99
R7929:Lrrc9	UTSW	12	72,533,071 (GRCm39)	missense	possibly damaging	0.92
R8042:Lrrc9	UTSW	12	72,507,680 (GRCm39)	missense	probably benign	0.02
R8108:Lrrc9	UTSW	12	72,500,833 (GRCm39)	missense	probably damaging	1.00
R8192:Lrrc9	UTSW	12	72,496,163 (GRCm39)	missense	probably damaging	1.00
R8244:Lrrc9	UTSW	12	72,546,384 (GRCm39)	missense	probably benign	0.22
R8333:Lrrc9	UTSW	12	72,528,317 (GRCm39)	missense	probably benign	0.38
R9288:Lrrc9	UTSW	12	72,522,858 (GRCm39)	missense	probably benign	0.01
R9324:Lrrc9	UTSW	12	72,496,171 (GRCm39)	missense	probably damaging	1.00
R9342:Lrrc9	UTSW	12	72,506,767 (GRCm39)	missense	probably damaging	1.00
R9557:Lrrc9	UTSW	12	72,532,981 (GRCm39)	missense	probably benign	0.01
R9624:Lrrc9	UTSW	12	72,497,586 (GRCm39)	missense	probably benign	0.19
R9677:Lrrc9	UTSW	12	72,497,539 (GRCm39)	missense	probably damaging	1.00
X0025:Lrrc9	UTSW	12	72,543,834 (GRCm39)	missense	probably damaging	1.00
Z1176:Lrrc9	UTSW	12	72,524,167 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGTCTGCTGTCAGCATCAGCATTTC -3'
(R):5'- ATGCACACATGCACACAGGATGGG -3'

Sequencing Primer
(F):5'- ccctcccttttccatcatcaatc -3'
(R):5'- GGAGTTAAGGATTTACTAGTTTGTCG -3'

Posted On

2013-04-16