Mutagenetix > Incidental Mutation

Incidental Mutation 'R6296:Lrch2'

508816

Institutional Source

Beutler Lab

Gene Symbol

Lrch2

Ensembl Gene

ENSMUSG00000031290

Gene Name

leucine-rich repeats and calponin homology (CH) domain containing 2

Synonyms

MMRRC Submission

044407-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.137) question?

Stock #

R6296 (G1)

Quality Score

221.999

Status

Not validated

Chromosome

Chromosomal Location

146253371-146337077 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 146263553 bp (GRCm39)

Zygosity

Homozygous

Amino Acid Change

Alanine to Threonine at position 369 (A369T)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000112819] [ENSMUST00000152838]

AlphaFold

Q3UMG5

Predicted Effect

probably damaging
Transcript: ENSMUST00000112819
AA Change: A679T

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

SMART Domains

Protein: ENSMUSP00000108438
Gene: ENSMUSG00000031290
AA Change: A679T

Domain	Start	End	E-Value	Type
low complexity region	6	52	N/A	INTRINSIC
LRR	141	163	7.59e1	SMART
LRR_TYP	164	187	4.11e-2	SMART
LRR	209	231	6.59e1	SMART
LRR	232	255	2.67e-1	SMART
LRR	277	300	3.36e1	SMART
low complexity region	437	454	N/A	INTRINSIC
low complexity region	462	477	N/A	INTRINSIC
low complexity region	580	593	N/A	INTRINSIC
CH	656	759	1.98e-14	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000122472

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134265

Predicted Effect

probably damaging
Transcript: ENSMUST00000136789
AA Change: A689T

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

SMART Domains

Protein: ENSMUSP00000123633
Gene: ENSMUSG00000031290
AA Change: A689T

Domain	Start	End	E-Value	Type
low complexity region	17	63	N/A	INTRINSIC
LRR	152	174	7.59e1	SMART
LRR_TYP	175	198	4.11e-2	SMART
LRR	220	242	6.59e1	SMART
LRR	243	266	2.67e-1	SMART
LRR	288	311	3.36e1	SMART
low complexity region	448	465	N/A	INTRINSIC
low complexity region	473	488	N/A	INTRINSIC
low complexity region	591	604	N/A	INTRINSIC
CH	667	770	1.98e-14	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000137665
AA Change: A369T

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

SMART Domains

Protein: ENSMUSP00000117458
Gene: ENSMUSG00000031290
AA Change: A369T

Domain	Start	End	E-Value	Type
low complexity region	150	167	N/A	INTRINSIC
low complexity region	175	190	N/A	INTRINSIC
low complexity region	271	284	N/A	INTRINSIC
CH	347	450	1.98e-14	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151730

Predicted Effect

probably damaging
Transcript: ENSMUST00000152838
AA Change: A358T

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000121128
Gene: ENSMUSG00000031290
AA Change: A358T

Domain	Start	End	E-Value	Type
low complexity region	133	150	N/A	INTRINSIC
low complexity region	158	173	N/A	INTRINSIC
CH	335	438	1.98e-14	SMART

Meta Mutation Damage Score

0.2226

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the leucine-rich repeat and calponin homology domain-containing protein family. These family members contain multiple N-terminal leucine-rich repeats, in addition to a C-terminal calponin homology domain, a type of domain that mediates interactions with actin filaments. These proteins are conserved across animal species, and studies of a similar Drosophila protein indicate a function as a cytoskeletal scaffolding protein. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2011]
PHENOTYPE: Male chimeras hemizygous for a gene trapped allele appear normal at E9.5. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933427D14Rik	T	C	11: 72,086,580 (GRCm39)	K277R	probably damaging	Het
Aatf	T	C	11: 84,363,926 (GRCm39)	Y267C	probably benign	Het
Adcy5	A	G	16: 35,124,080 (GRCm39)	Y1253C	probably damaging	Het
Adgra3	G	A	5: 50,118,189 (GRCm39)	P1120S	probably benign	Het
Adm	A	G	7: 110,227,561 (GRCm39)	T26A	probably benign	Het
Ahnak	T	G	19: 8,980,669 (GRCm39)	V651G	probably damaging	Het
Akr7a5	G	A	4: 139,045,532 (GRCm39)	V358I	probably benign	Het
Ankar	T	G	1: 72,682,417 (GRCm39)	T1383P	probably damaging	Het
Bpifb6	G	C	2: 153,748,812 (GRCm39)	K269N	possibly damaging	Het
Cacna1c	T	C	6: 118,575,684 (GRCm39)	E1927G	possibly damaging	Het
Cacna1c	T	A	6: 118,629,675 (GRCm39)	T1249S	probably benign	Het
Cacna1h	G	A	17: 25,602,053 (GRCm39)	R1596C	probably damaging	Het
Cbll1	A	G	12: 31,537,507 (GRCm39)	V415A	probably benign	Het
Cd300lf	C	T	11: 115,015,195 (GRCm39)	V132I	probably benign	Het
Cfap54	T	C	10: 92,902,708 (GRCm39)	Y148C	probably damaging	Het
Coa5	A	G	1: 37,467,428 (GRCm39)	S60P	probably damaging	Het
Col6a2	T	C	10: 76,446,883 (GRCm39)	N342D	probably damaging	Het
Cyp2c29	T	G	19: 39,318,705 (GRCm39)	I434S	possibly damaging	Het
Ddx11	G	A	17: 66,457,724 (GRCm39)		probably null	Het
Dgke	C	T	11: 88,931,575 (GRCm39)	V560I	probably benign	Het
Dusp16	C	A	6: 134,697,456 (GRCm39)		probably null	Het
Enpp4	G	T	17: 44,413,371 (GRCm39)	N54K	probably benign	Het
Epn1	G	A	7: 5,093,122 (GRCm39)	A145T	probably damaging	Het
Erc2	A	T	14: 27,802,112 (GRCm39)	K764M	probably damaging	Het
Ercc6	G	T	14: 32,248,360 (GRCm39)	E304*	probably null	Het
Fam117a	T	A	11: 95,254,971 (GRCm39)	C115S	possibly damaging	Het
Galntl5	T	C	5: 25,391,163 (GRCm39)	S21P	probably benign	Het
Gm6358	T	C	16: 88,937,970 (GRCm39)	S70P	unknown	Het
Grip1	C	T	10: 119,911,369 (GRCm39)	Q696*	probably null	Het
Haus5	C	T	7: 30,358,401 (GRCm39)	W298*	probably null	Het
Hsfy2	T	A	1: 56,676,351 (GRCm39)	H62L	probably benign	Het
Ighm	T	C	12: 113,385,187 (GRCm39)	I258V	unknown	Het
Igkv13-71-1	G	T	6: 69,212,783 (GRCm39)		noncoding transcript	Het
Inava	C	T	1: 136,148,809 (GRCm39)		probably null	Het
Irx1	A	C	13: 72,107,787 (GRCm39)	S298R	probably damaging	Het
Jarid2	T	A	13: 45,056,539 (GRCm39)	Y443N	possibly damaging	Het
Kcnc1	G	A	7: 46,084,740 (GRCm39)	A555T	probably benign	Het
Krtap4-6	T	A	11: 99,556,245 (GRCm39)	R161*	probably null	Het
Lipo3	T	C	19: 33,757,737 (GRCm39)	D244G	probably benign	Het
Lmo2	T	G	2: 103,800,946 (GRCm39)	V39G	possibly damaging	Het
Macf1	A	T	4: 123,326,668 (GRCm39)	I4943N	probably damaging	Het
Mkx	A	T	18: 7,000,591 (GRCm39)		probably null	Het
Nek1	C	T	8: 61,525,343 (GRCm39)	Q594*	probably null	Het
Nipbl	T	C	15: 8,330,379 (GRCm39)	M2349V	possibly damaging	Het
Nup155	T	A	15: 8,182,639 (GRCm39)	C1201S	probably damaging	Het
Or2y8	C	A	11: 52,035,423 (GRCm39)	R311S	probably benign	Het
Or4a76	G	A	2: 89,460,975 (GRCm39)	T89I	probably damaging	Het
Or5ac25	T	C	16: 59,181,769 (GRCm39)	K271E	probably benign	Het
Osbpl1a	A	G	18: 12,952,560 (GRCm39)		probably null	Het
Pbx1	T	C	1: 168,011,184 (GRCm39)	D372G	possibly damaging	Het
Pikfyve	T	A	1: 65,302,112 (GRCm39)	S1668T	probably damaging	Het
Pitpnc1	T	C	11: 107,117,092 (GRCm39)	H193R	probably damaging	Het
Plag1	G	T	4: 3,904,499 (GRCm39)	H231N	probably damaging	Het
Prmt8	A	G	6: 127,688,767 (GRCm39)	I201T	probably damaging	Het
Ptpn23	A	T	9: 110,222,894 (GRCm39)	N54K	probably damaging	Het
Rab11fip4	T	C	11: 79,581,655 (GRCm39)		probably null	Het
Rassf9	T	A	10: 102,381,614 (GRCm39)	I332N	probably damaging	Het
Rgs9	T	C	11: 109,159,813 (GRCm39)	N173S	probably benign	Het
Rhbdl1	A	G	17: 26,053,943 (GRCm39)	L309P	probably damaging	Het
Rnf214	A	G	9: 45,779,119 (GRCm39)	S389P	probably benign	Het
Rxfp1	A	C	3: 79,575,155 (GRCm39)	L181R	probably damaging	Het
Sfxn1	C	T	13: 54,247,899 (GRCm39)	T208I	probably benign	Het
Sgo2b	C	T	8: 64,380,827 (GRCm39)	M668I	probably benign	Het
Sh3bp4	C	A	1: 89,073,211 (GRCm39)	S686R	probably damaging	Het
Spata31d1d	G	A	13: 59,876,278 (GRCm39)	T419I	possibly damaging	Het
Spata31d1e	T	C	13: 59,890,497 (GRCm39)	D441G	probably benign	Het
Spink5	T	C	18: 44,147,824 (GRCm39)	S857P	probably damaging	Het
Stard13	A	T	5: 150,986,138 (GRCm39)	S339R	probably damaging	Het
Stk35	T	A	2: 129,652,808 (GRCm39)	Y436*	probably null	Het
Supt6	C	T	11: 78,116,885 (GRCm39)	R589Q	possibly damaging	Het
Tinag	T	A	9: 76,904,217 (GRCm39)	E402V	possibly damaging	Het
Tmem183a	T	C	1: 134,289,349 (GRCm39)	D27G	probably damaging	Het
Tnfrsf13c	T	C	15: 82,108,103 (GRCm39)	T56A	probably damaging	Het
Tnrc18	A	C	5: 142,719,331 (GRCm39)	L1985R	unknown	Het
Ttn	G	A	2: 76,579,673 (GRCm39)	T23740M	probably damaging	Het
Ufl1	G	T	4: 25,270,572 (GRCm39)	Q215K	probably benign	Het
Unkl	T	C	17: 25,450,839 (GRCm39)	*232R	probably null	Het
Wnk4	A	T	11: 101,164,824 (GRCm39)	N718Y	probably damaging	Het
Xkr4	T	C	1: 3,286,793 (GRCm39)	T466A	probably benign	Het
Zfp451	T	A	1: 33,808,898 (GRCm39)	K988*	probably null	Het
Zfp503	G	C	14: 22,035,868 (GRCm39)	Y349*	probably null	Het
Zfp990	T	A	4: 145,264,673 (GRCm39)	F557Y	possibly damaging	Het

Other mutations in Lrch2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02151:Lrch2	APN	X	146,336,716 (GRCm39)	missense	possibly damaging	0.75
IGL02619:Lrch2	APN	X	146,302,131 (GRCm39)	missense	probably damaging	1.00
IGL02619:Lrch2	APN	X	146,263,537 (GRCm39)	missense	probably damaging	1.00
R2920:Lrch2	UTSW	X	146,256,026 (GRCm39)	missense	probably damaging	1.00
R3885:Lrch2	UTSW	X	146,256,003 (GRCm39)	missense	probably damaging	1.00
R3886:Lrch2	UTSW	X	146,256,003 (GRCm39)	missense	probably damaging	1.00
R6293:Lrch2	UTSW	X	146,263,553 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ACATTTTGCCATGCTCAGCTTG -3'
(R):5'- ACAGGAACGGGTTTAATTCAGC -3'

Sequencing Primer
(F):5'- GAGACACACATGATAAGTACTCTTC -3'
(R):5'- GGAACGGGTTTAATTCAGCAAATTC -3'

Posted On

2018-04-02