Mutagenetix > Incidental Mutation

Incidental Mutation 'R2313:Lrch3'

245387

Institutional Source

Beutler Lab

Gene Symbol

Lrch3

Ensembl Gene

ENSMUSG00000022801

Gene Name

leucine-rich repeats and calponin homology (CH) domain containing 3

Synonyms

LOC385628, 2210409B11Rik

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.115) question?

Stock #

R2313 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

32734470-32836017 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 32782045 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 273 (N273S)

Ref Sequence

ENSEMBL: ENSMUSP00000126964 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000023491] [ENSMUST00000135193] [ENSMUST00000164486] [ENSMUST00000165616] [ENSMUST00000170201] [ENSMUST00000170899]

AlphaFold

Q8BVU0

Predicted Effect

probably damaging
Transcript: ENSMUST00000023491
AA Change: N273S

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000023491
Gene: ENSMUSG00000022801
AA Change: N273S

Domain	Start	End	E-Value	Type
low complexity region	2	13	N/A	INTRINSIC
low complexity region	31	44	N/A	INTRINSIC
LRR	104	126	2.54e1	SMART
LRR	127	150	2.86e-1	SMART
LRR	172	194	4.44e0	SMART
LRR	195	218	4.33e1	SMART
LRR	240	263	2.76e1	SMART
low complexity region	482	493	N/A	INTRINSIC
low complexity region	539	554	N/A	INTRINSIC
CH	651	754	9.24e-15	SMART
low complexity region	759	774	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000133399

Predicted Effect

probably damaging
Transcript: ENSMUST00000135193
AA Change: N273S

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

SMART Domains

Protein: ENSMUSP00000130708
Gene: ENSMUSG00000022801
AA Change: N273S

Domain	Start	End	E-Value	Type
low complexity region	2	13	N/A	INTRINSIC
low complexity region	31	44	N/A	INTRINSIC
LRR	104	126	2.54e1	SMART
LRR	127	150	2.86e-1	SMART
LRR	172	194	4.44e0	SMART
LRR	195	218	4.33e1	SMART
LRR	240	263	2.76e1	SMART
low complexity region	482	493	N/A	INTRINSIC
low complexity region	539	554	N/A	INTRINSIC
CH	651	755	6.79e-13	SMART
transmembrane domain	771	793	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156928

Predicted Effect

probably benign
Transcript: ENSMUST00000164486

SMART Domains

Protein: ENSMUSP00000131416
Gene: ENSMUSG00000022801

Domain	Start	End	E-Value	Type
low complexity region	2	13	N/A	INTRINSIC
low complexity region	31	44	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000165616
AA Change: N147S

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000130009
Gene: ENSMUSG00000022801
AA Change: N147S

Domain	Start	End	E-Value	Type
low complexity region	2	13	N/A	INTRINSIC
low complexity region	31	44	N/A	INTRINSIC
Blast:LRR	89	113	1e-6	BLAST
Blast:LRR	114	137	3e-7	BLAST
low complexity region	328	339	N/A	INTRINSIC
low complexity region	385	400	N/A	INTRINSIC
CH	497	600	9.24e-15	SMART
low complexity region	605	620	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000170201
AA Change: N273S

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

SMART Domains

Protein: ENSMUSP00000126964
Gene: ENSMUSG00000022801
AA Change: N273S

Domain	Start	End	E-Value	Type
low complexity region	2	13	N/A	INTRINSIC
low complexity region	31	44	N/A	INTRINSIC
LRR	104	126	2.54e1	SMART
LRR	127	150	2.86e-1	SMART
LRR	172	194	4.44e0	SMART
LRR	195	218	4.33e1	SMART
LRR	240	263	2.76e1	SMART
low complexity region	482	493	N/A	INTRINSIC
low complexity region	539	554	N/A	INTRINSIC
CH	615	718	9.24e-15	SMART
low complexity region	723	738	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000170899
AA Change: N273S

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000127547
Gene: ENSMUSG00000022801
AA Change: N273S

Domain	Start	End	E-Value	Type
low complexity region	2	13	N/A	INTRINSIC
low complexity region	31	44	N/A	INTRINSIC
LRR	104	126	2.54e1	SMART
LRR	127	150	2.86e-1	SMART
LRR	172	194	4.44e0	SMART
LRR	195	218	4.33e1	SMART
LRR	240	263	2.76e1	SMART
low complexity region	489	504	N/A	INTRINSIC
CH	565	668	9.24e-15	SMART
low complexity region	673	688	N/A	INTRINSIC

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.1%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 21 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Alox5	T	A	6: 116,390,822 (GRCm39)	D443V	probably benign	Het
Ankrd53	A	T	6: 83,740,662 (GRCm39)	H95L	probably damaging	Het
Chrnb3	A	G	8: 27,883,809 (GRCm39)	Y182C	probably damaging	Het
Cln5	C	T	14: 103,309,182 (GRCm39)	R79*	probably null	Het
Cntn3	C	A	6: 102,180,889 (GRCm39)	V769L	probably benign	Het
Gpat4	G	A	8: 23,670,171 (GRCm39)	P286L	probably damaging	Het
Il1r1	T	C	1: 40,352,470 (GRCm39)	S550P	probably benign	Het
Klra7	T	A	6: 130,205,505 (GRCm39)	T132S	probably benign	Het
Lrriq3	A	T	3: 154,869,660 (GRCm39)	R328S	probably benign	Het
Mpp2	T	C	11: 101,952,898 (GRCm39)	E318G	possibly damaging	Het
Or4c122	C	A	2: 89,079,285 (GRCm39)	C239F	probably damaging	Het
Or4n4	G	A	14: 50,519,431 (GRCm39)	S93F	probably damaging	Het
Pglyrp2	A	T	17: 32,637,673 (GRCm39)	D118E	probably damaging	Het
Ppp4c	A	G	7: 126,386,629 (GRCm39)	S153P	probably damaging	Het
Ptpn13	A	G	5: 103,712,027 (GRCm39)	S1642G	probably damaging	Het
Tmem59l	A	G	8: 70,939,951 (GRCm39)	L6S	unknown	Het
Unc13d	A	G	11: 115,954,560 (GRCm39)	F1016S	probably damaging	Het
Vwa8	C	G	14: 79,149,658 (GRCm39)	T140S	probably damaging	Het
Wdfy3	A	G	5: 102,037,150 (GRCm39)	F2046L	probably damaging	Het
Zfp788	A	G	7: 41,298,312 (GRCm39)	H316R	probably damaging	Het
Zfp994	T	A	17: 22,420,266 (GRCm39)	I228F	probably damaging	Het

Other mutations in Lrch3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01129:Lrch3	APN	16	32,815,335 (GRCm39)	missense	probably benign	0.10
IGL01400:Lrch3	APN	16	32,799,911 (GRCm39)	missense	probably damaging	1.00
IGL02565:Lrch3	APN	16	32,826,084 (GRCm39)	missense	probably benign	0.00
IGL03076:Lrch3	APN	16	32,802,223 (GRCm39)	missense	possibly damaging	0.52
IGL03103:Lrch3	APN	16	32,772,507 (GRCm39)	missense	probably damaging	1.00
IGL03125:Lrch3	APN	16	32,734,647 (GRCm39)	missense	possibly damaging	0.83
IGL03349:Lrch3	APN	16	32,775,694 (GRCm39)	missense	probably damaging	1.00
eluted	UTSW	16	32,806,377 (GRCm39)	missense	probably null
leached	UTSW	16	32,779,833 (GRCm39)	missense	probably damaging	1.00
R0054:Lrch3	UTSW	16	32,816,222 (GRCm39)	intron	probably benign
R0123:Lrch3	UTSW	16	32,782,124 (GRCm39)	splice site	probably benign
R0225:Lrch3	UTSW	16	32,782,124 (GRCm39)	splice site	probably benign
R0326:Lrch3	UTSW	16	32,799,870 (GRCm39)	missense	probably damaging	1.00
R0455:Lrch3	UTSW	16	32,807,250 (GRCm39)	missense	probably damaging	0.99
R0734:Lrch3	UTSW	16	32,817,853 (GRCm39)	nonsense	probably null
R1204:Lrch3	UTSW	16	32,829,584 (GRCm39)	missense	probably damaging	1.00
R1470:Lrch3	UTSW	16	32,808,865 (GRCm39)	splice site	probably benign
R1526:Lrch3	UTSW	16	32,770,746 (GRCm39)	missense	probably damaging	1.00
R1597:Lrch3	UTSW	16	32,770,781 (GRCm39)	nonsense	probably null
R1850:Lrch3	UTSW	16	32,807,163 (GRCm39)	missense	probably benign	0.01
R1966:Lrch3	UTSW	16	32,734,755 (GRCm39)	missense	possibly damaging	0.94
R2241:Lrch3	UTSW	16	32,816,211 (GRCm39)	missense	probably damaging	0.99
R2902:Lrch3	UTSW	16	32,770,766 (GRCm39)	missense	probably damaging	1.00
R4723:Lrch3	UTSW	16	32,808,854 (GRCm39)	splice site	probably null
R4795:Lrch3	UTSW	16	32,826,074 (GRCm39)	missense	probably damaging	1.00
R4970:Lrch3	UTSW	16	32,818,883 (GRCm39)	missense	probably damaging	1.00
R5223:Lrch3	UTSW	16	32,734,767 (GRCm39)	missense	probably damaging	0.99
R5292:Lrch3	UTSW	16	32,796,177 (GRCm39)	missense	probably damaging	1.00
R5414:Lrch3	UTSW	16	32,806,335 (GRCm39)	splice site	probably null
R5470:Lrch3	UTSW	16	32,818,960 (GRCm39)	missense	probably damaging	1.00
R5594:Lrch3	UTSW	16	32,734,554 (GRCm39)	missense	probably damaging	0.99
R5843:Lrch3	UTSW	16	32,818,896 (GRCm39)	missense	probably damaging	1.00
R5862:Lrch3	UTSW	16	32,816,179 (GRCm39)	missense	probably damaging	1.00
R5911:Lrch3	UTSW	16	32,779,833 (GRCm39)	missense	probably damaging	1.00
R5932:Lrch3	UTSW	16	32,796,106 (GRCm39)	missense	probably damaging	1.00
R6519:Lrch3	UTSW	16	32,815,367 (GRCm39)	critical splice donor site	probably benign
R6731:Lrch3	UTSW	16	32,770,790 (GRCm39)	missense	probably damaging	1.00
R7182:Lrch3	UTSW	16	32,814,149 (GRCm39)	missense	probably benign	0.05
R7197:Lrch3	UTSW	16	32,810,665 (GRCm39)	missense	probably damaging	1.00
R7319:Lrch3	UTSW	16	32,815,363 (GRCm39)	missense	probably benign	0.19
R7392:Lrch3	UTSW	16	32,807,125 (GRCm39)	nonsense	probably null
R7408:Lrch3	UTSW	16	32,807,113 (GRCm39)	nonsense	probably null
R7414:Lrch3	UTSW	16	32,818,883 (GRCm39)	missense	probably damaging	1.00
R7425:Lrch3	UTSW	16	32,826,077 (GRCm39)	missense	probably damaging	1.00
R7909:Lrch3	UTSW	16	32,829,663 (GRCm39)	missense	probably benign	0.00
R7956:Lrch3	UTSW	16	32,806,377 (GRCm39)	missense	probably null
R8009:Lrch3	UTSW	16	32,826,083 (GRCm39)	missense	possibly damaging	0.72
R8247:Lrch3	UTSW	16	32,829,713 (GRCm39)	nonsense	probably null
R8408:Lrch3	UTSW	16	32,775,750 (GRCm39)	missense	probably damaging	1.00
R8686:Lrch3	UTSW	16	32,802,223 (GRCm39)	missense	possibly damaging	0.52
R8756:Lrch3	UTSW	16	32,808,810 (GRCm39)	missense	probably benign	0.33
R8947:Lrch3	UTSW	16	32,802,199 (GRCm39)	missense	possibly damaging	0.66
R9459:Lrch3	UTSW	16	32,799,775 (GRCm39)	missense	probably damaging	0.99
R9710:Lrch3	UTSW	16	32,796,108 (GRCm39)	nonsense	probably null
Z1176:Lrch3	UTSW	16	32,734,686 (GRCm39)	missense	possibly damaging	0.89

Predicted Primers

PCR Primer
(F):5'- AAGTCCTGGCTGTGTACAAC -3'
(R):5'- GACTTTGACTACACTTGGTGGG -3'

Sequencing Primer
(F):5'- GTCCTGGCTGTGTACAACTAATCAG -3'
(R):5'- CTACACTTGGTGGGATCTATATAACC -3'

Posted On

2014-10-30