Mutagenetix > Incidental Mutations

Incidental Mutation 'R1955:Lrit3'

217650

Institutional Source

Beutler Lab

Gene Symbol

Lrit3

Ensembl Gene

ENSMUSG00000093865

Gene Name

leucine-rich repeat, immunoglobulin-like and transmembrane domains 3

Synonyms

LOC242235

MMRRC Submission

039969-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1955 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

129787881-129804030 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 129800481 bp

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 149 (V149A)

Ref Sequence

ENSEMBL: ENSMUSP00000140184 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000171313] [ENSMUST00000179187] [ENSMUST00000185462]

Predicted Effect

probably benign
Transcript: ENSMUST00000171313

SMART Domains

Protein: ENSMUSP00000132360
Gene: ENSMUSG00000028012

Domain	Start	End	E-Value	Type
low complexity region	6	22	N/A	INTRINSIC
Pfam:7TM_GPCR_Srsx	36	309	3.5e-11	PFAM
Pfam:7tm_1	42	294	4.6e-45	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000179187
AA Change: V149A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000136912
Gene: ENSMUSG00000093865
AA Change: V149A

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
LRRNT	20	61	2.7e-1	SMART
LRR	80	103	6.96e0	SMART
LRR	104	127	3.27e1	SMART
LRR_TYP	128	151	4.47e-3	SMART
LRR_TYP	152	175	7.37e-4	SMART
LRRCT	201	252	4.65e-2	SMART
Blast:IG	260	297	9e-13	BLAST
low complexity region	298	311	N/A	INTRINSIC
FN3	364	443	1.85e0	SMART
transmembrane domain	462	484	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000185462
AA Change: V149A

PolyPhen 2 Score 0.108 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000140184
Gene: ENSMUSG00000093865
AA Change: V149A

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
LRRNT	20	61	1.3e-3	SMART
LRR	80	103	2.9e-2	SMART
LRR	104	127	1.4e-1	SMART
LRR_TYP	128	151	1.9e-5	SMART
LRR_TYP	152	175	3.2e-6	SMART
LRRCT	201	252	2.3e-4	SMART
IGc2	266	335	4.7e-11	SMART
low complexity region	340	352	N/A	INTRINSIC
low complexity region	362	376	N/A	INTRINSIC
low complexity region	408	432	N/A	INTRINSIC
FN3	485	564	9e-3	SMART
transmembrane domain	583	605	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000188978

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000196317

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.9%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that has a fibronectin type III domain and a C-terminal transmembrane domain, as well as a leucine-rich repeat domain and immunoglobulin-like domain near the N-terminus. The encoded protein may regulate fibroblast growth factor receptors and affect the modification of these receptors, which are glycosylated differently in the Golgi and endoplasmic reticulum. Mutations in this gene are associated with congenital stationary night blindness, type 1F. [provided by RefSeq, May 2013]
PHENOTYPE: Mice homozygous for a targeted allele show a selective absence of the ERG b-wave with a normal a-wave component under scotopic conditions, as well as variable ERG responses with larger a-wave amplitudes, shorter b-wave amplitudes, and longer implicit times of both waves under photopic conditions. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 101 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700019A02Rik	T	A	1: 53,163,241	K128N	probably benign	Het
4930430F08Rik	A	G	10: 100,577,304	V91A	probably damaging	Het
Acadm	A	C	3: 153,929,551	F309V	probably damaging	Het
Adam6b	C	A	12: 113,491,816	A751E	probably benign	Het
Adcy9	A	G	16: 4,418,659	I296T	possibly damaging	Het
Arhgap45	A	G	10: 80,026,492	E471G	probably benign	Het
Atcay	T	C	10: 81,214,793	D96G	possibly damaging	Het
B3galt4	T	A	17: 33,950,632	R211*	probably null	Het
Bpi	T	C	2: 158,274,715	I344T	probably damaging	Het
Btnl4	T	C	17: 34,472,930	K233E	possibly damaging	Het
Cars2	A	T	8: 11,550,286	Y68N	probably damaging	Het
Cd207	T	A	6: 83,671,775	R302W	probably benign	Het
Cdc5l	T	C	17: 45,426,516		probably null	Het
Chaf1a	C	T	17: 56,047,540	T270I	unknown	Het
Col4a1	C	T	8: 11,208,228		probably null	Het
Col7a1	G	T	9: 108,955,664	V187L	unknown	Het
Cry1	G	A	10: 85,144,178	T422I	probably benign	Het
Csgalnact1	C	T	8: 68,372,667	V392I	probably benign	Het
Cyp2c38	A	G	19: 39,404,687	L312P	probably damaging	Het
Ddx20	G	A	3: 105,679,562	T489M	possibly damaging	Het
Decr1	A	T	4: 15,924,256	N221K	probably benign	Het
Dennd4a	A	T	9: 64,852,467	T285S	probably benign	Het
Dgka	A	G	10: 128,730,189		probably null	Het
Dmd	A	T	X: 83,878,557	M1478L	probably benign	Het
Dvl1	G	A	4: 155,858,029	R584Q	possibly damaging	Het
Dync1li1	A	T	9: 114,721,746	S450C	probably damaging	Het
Ehbp1l1	A	G	19: 5,710,669	V1558A	possibly damaging	Het
Esr1	T	A	10: 4,857,125	M347K	probably damaging	Het
F2	T	A	2: 91,633,095	H148L	probably benign	Het
Fezf2	T	C	14: 12,342,644	N407S	probably benign	Het
Fscn3	T	A	6: 28,430,236	M135K	possibly damaging	Het
Ganab	T	G	19: 8,911,616	Y560*	probably null	Het
Garem2	T	C	5: 30,108,270	V44A	probably benign	Het
Gja4	A	G	4: 127,312,449	W174R	probably damaging	Het
Gja5	A	T	3: 97,051,641	H338L	probably benign	Het
Gm43517	A	G	12: 49,389,889		probably benign	Het
Gm5434	A	G	12: 36,090,596		probably benign	Het
Iqch	A	T	9: 63,548,016	D166E	probably benign	Het
Kifc5b	T	A	17: 26,926,297		probably null	Het
Kmt2b	A	T	7: 30,575,351	M1976K	possibly damaging	Het
Leng1	A	T	7: 3,665,416	V11D	probably damaging	Het
Lrpap1	A	G	5: 35,102,412	L114P	probably damaging	Het
Marveld3	T	A	8: 109,959,748	D162V	probably benign	Het
Mon2	A	T	10: 123,038,483	I320N	probably damaging	Het
Morc2b	T	C	17: 33,137,490	Y436C	probably damaging	Het
Myo7a	A	T	7: 98,054,921	V1928D	probably damaging	Het
Ncoa6	A	G	2: 155,406,821	V1521A	possibly damaging	Het
Nexmif	A	G	X: 104,083,953	S1453P	possibly damaging	Het
Nudt16l1	A	G	16: 4,940,325	M182V	probably benign	Het
Obp2b	A	T	2: 25,738,551	I106L	probably benign	Het
Olfr1129	T	A	2: 87,576,005	L307Q	probably damaging	Het
Olfr1239	T	A	2: 89,418,411	M1L	probably damaging	Het
Olfr186	T	A	16: 59,027,411	R165S	probably damaging	Het
Olfr902	T	C	9: 38,449,688	I272T	probably benign	Het
Parl	T	A	16: 20,302,327	M1L	possibly damaging	Het
Pde7a	G	A	3: 19,227,799	A429V	probably damaging	Het
Pkd1l2	T	A	8: 117,043,361	M1119L	probably benign	Het
Plch1	C	T	3: 63,755,267	V272I	probably damaging	Het
Plekha4	G	A	7: 45,553,906	G740D	probably damaging	Het
Pnliprp1	A	G	19: 58,734,972	D265G	possibly damaging	Het
Pola1	A	C	X: 93,597,261	V384G	probably damaging	Het
Pon3	T	A	6: 5,230,774	D251V	probably benign	Het
Pot1b	A	G	17: 55,674,067	C316R	possibly damaging	Het
Prkaca	T	A	8: 83,988,317	V116E	probably damaging	Het
Prpf6	T	G	2: 181,632,077	M338R	probably benign	Het
Rasgef1c	A	G	11: 49,975,715	H382R	possibly damaging	Het
Rps25	C	T	9: 44,410,008	T113I	probably benign	Het
Serpinb1b	G	T	13: 33,085,439	A52S	probably benign	Het
Sh3yl1	A	G	12: 30,922,333	K34E	possibly damaging	Het
Siah2	C	T	3: 58,676,097	R256Q	probably damaging	Het
Slc24a2	A	G	4: 87,073,244	L404P	probably damaging	Het
Slc28a2	G	A	2: 122,447,866	C122Y	probably benign	Het
Slc4a8	T	C	15: 100,807,376	I821T	probably damaging	Het
Slc5a3	T	C	16: 92,077,874	V273A	possibly damaging	Het
Spag7	T	C	11: 70,665,018	Q61R	probably benign	Het
Syt7	A	T	19: 10,418,038	I71F	probably damaging	Het
Tars2	T	C	3: 95,747,454	N413S	probably damaging	Het
Tex14	T	A	11: 87,509,621	L413Q	probably damaging	Het
Tjp3	T	C	10: 81,277,999	E475G	probably damaging	Het
Tmem131l	A	G	3: 83,961,544	S175P	probably damaging	Het
Tmem144	C	T	3: 79,826,857	V180M	probably benign	Het
Tmem200c	A	T	17: 68,840,961	I180F	probably damaging	Het
Tmem232	G	T	17: 65,484,487	H129N	probably benign	Het
Tmprss11g	T	A	5: 86,498,532	I59F	probably damaging	Het
Tmprss2	T	A	16: 97,567,177		probably null	Het
Tor1aip2	T	A	1: 156,051,842		probably benign	Het
Trim61	T	C	8: 65,013,392	I406V	possibly damaging	Het
Trpv5	T	C	6: 41,657,937	D486G	probably damaging	Het
Try5	T	C	6: 41,311,769	E64G	probably benign	Het
Txlnb	A	G	10: 17,799,420	E107G	probably damaging	Het
Uckl1	T	C	2: 181,570,527	Q332R	probably benign	Het
Ugt2b1	T	C	5: 86,917,713	Y489C	probably damaging	Het
Ugt2b5	T	A	5: 87,127,772	M407L	probably benign	Het
Vmn1r191	A	T	13: 22,178,815	S256R	possibly damaging	Het
Vps13b	T	G	15: 35,925,408		probably null	Het
Vps13d	A	G	4: 145,156,143	F960S	probably damaging	Het
Xab2	T	A	8: 3,616,094	D227V	probably damaging	Het
Xaf1	A	T	11: 72,306,606	D136V	possibly damaging	Het
Zan	A	G	5: 137,389,283	S4889P	unknown	Het
Zfp78	A	G	7: 6,378,559	T203A	probably benign	Het
Zfp821	T	C	8: 109,721,242	S72P	probably damaging	Het

Other mutations in Lrit3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
FR4304:Lrit3	UTSW	3	129788819	small insertion	probably benign
FR4340:Lrit3	UTSW	3	129788808	small insertion	probably benign
FR4548:Lrit3	UTSW	3	129788813	small insertion	probably benign
FR4548:Lrit3	UTSW	3	129788816	small insertion	probably benign
FR4589:Lrit3	UTSW	3	129803913	frame shift	probably null
FR4737:Lrit3	UTSW	3	129788806	small insertion	probably benign
FR4737:Lrit3	UTSW	3	129788810	small insertion	probably benign
FR4737:Lrit3	UTSW	3	129803913	frame shift	probably null
FR4976:Lrit3	UTSW	3	129803910	unclassified	probably benign
R0555:Lrit3	UTSW	3	129791296	missense	probably damaging	1.00
R0629:Lrit3	UTSW	3	129788302	missense	probably damaging	1.00
R0631:Lrit3	UTSW	3	129788555	missense	probably damaging	1.00
R1690:Lrit3	UTSW	3	129800745	missense	probably damaging	0.99
R1902:Lrit3	UTSW	3	129791246	missense	probably benign	0.17
R3155:Lrit3	UTSW	3	129791395	missense	probably benign	0.00
R4005:Lrit3	UTSW	3	129791372	missense	probably benign	0.14
R4445:Lrit3	UTSW	3	129788531	nonsense	probably null
R4675:Lrit3	UTSW	3	129788472	missense	probably damaging	1.00
R5104:Lrit3	UTSW	3	129788391	missense	possibly damaging	0.86
R5147:Lrit3	UTSW	3	129803925	missense	possibly damaging	0.78
R5271:Lrit3	UTSW	3	129788301	missense	probably damaging	1.00
R5505:Lrit3	UTSW	3	129791438	missense	possibly damaging	0.83
R5587:Lrit3	UTSW	3	129788898	missense	probably benign	0.25
R6056:Lrit3	UTSW	3	129789355	missense	probably damaging	1.00
R6239:Lrit3	UTSW	3	129800346	missense	probably damaging	0.98
R6280:Lrit3	UTSW	3	129788763	missense	probably damaging	0.99
R6305:Lrit3	UTSW	3	129800460	missense	probably damaging	0.98
R6441:Lrit3	UTSW	3	129800360	missense	probably benign
R6947:Lrit3	UTSW	3	129789234	missense	probably benign	0.01
R6949:Lrit3	UTSW	3	129789285	missense	probably damaging	1.00
R7850:Lrit3	UTSW	3	129800803	missense	probably damaging	1.00
R8157:Lrit3	UTSW	3	129800635	missense	probably benign	0.00
R8405:Lrit3	UTSW	3	129788652	missense	probably benign	0.26

Predicted Primers

PCR Primer
(F):5'- AAGATCCCAGGTTAGATCCCC -3'
(R):5'- TGGCCAGCATAGAAACCAGTAG -3'

Sequencing Primer
(F):5'- AGGTTAGATCCCCATTGTTACACAC -3'
(R):5'- GTAGCTTCTATAACCTGAGGCAGC -3'

Posted On

2014-08-01