Mutagenetix > Incidental Mutations

Incidental Mutation 'R1445:Lrat'

158762

Institutional Source

Beutler Lab

Gene Symbol

Lrat

Ensembl Gene

ENSMUSG00000028003

Gene Name

lecithin-retinol acyltransferase (phosphatidylcholine-retinol-O-acyltransferase)

Synonyms

MMRRC Submission

039500-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.113) question?

Stock #

R1445 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

82892579-82903973 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 82903369 bp

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Alanine at position 115 (D115A)

Ref Sequence

ENSEMBL: ENSMUSP00000029632 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029632]

AlphaFold

Q9JI60

PDB Structure

Crystal structure of HRASLS3/LRAT chimeric protein [X-RAY DIFFRACTION]

Predicted Effect

probably damaging
Transcript: ENSMUST00000029632
AA Change: D115A

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

SMART Domains

Protein: ENSMUSP00000029632
Gene: ENSMUSG00000028003
AA Change: D115A

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
Pfam:LRAT	43	174	1.4e-44	PFAM
low complexity region	194	205	N/A	INTRINSIC
transmembrane domain	206	228	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131274

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147649

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149223

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156457

Meta Mutation Damage Score

0.6395

Coding Region Coverage

1x: 98.8%
3x: 97.7%
10x: 93.9%
20x: 84.0%

Validation Efficiency

96% (101/105)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene localizes to the endoplasmic reticulum, where it catalyzes the esterification of all-trans-retinol into all-trans-retinyl ester. This reaction is an important step in vitamin A metabolism in the visual system. Mutations in this gene have been associated with early-onset severe retinal dystrophy and Leber congenital amaurosis 14. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2014]
PHENOTYPE: Mice homozygous for disruptions in this gene exhibit retinol homeostasis abnormalities and are more susceptible to vitamin A deficiency or display impaired vision associated with abnormal retinol metabolism. Males have testicular hypoplasia/atrophy and reduced mature sperm counts. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 94 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700061I17Rik	G	T	3: 117,067,736		noncoding transcript	Het
2300003K06Rik	G	T	11: 99,837,967	Q17K	probably benign	Het
Abca16	T	C	7: 120,520,033	V999A	probably benign	Het
Actn3	C	T	19: 4,865,455		probably benign	Het
Agap2	T	A	10: 127,091,112		probably benign	Het
Ago3	C	A	4: 126,371,787	R278L	probably benign	Het
Aldh1a2	T	C	9: 71,285,210	V449A	possibly damaging	Het
Alkbh2	C	T	5: 114,124,226	E148K	probably damaging	Het
Aplnr	A	G	2: 85,137,009	Y126C	probably damaging	Het
Apob	T	C	12: 8,016,084	I4351T	possibly damaging	Het
Ash1l	T	C	3: 89,007,352	L1763P	probably benign	Het
Aspn	T	C	13: 49,557,373	S165P	possibly damaging	Het
Atg13	A	T	2: 91,679,990	V349E	probably damaging	Het
Atp1b2	T	A	11: 69,602,483		probably null	Het
B3glct	A	T	5: 149,754,139	D411V	probably damaging	Het
Bcar3	A	T	3: 122,523,191	I255F	probably damaging	Het
Cacna1b	G	A	2: 24,718,136		probably benign	Het
Cep164	T	G	9: 45,778,900	E675A	possibly damaging	Het
Chd1l	C	T	3: 97,582,731	E503K	probably benign	Het
Chst8	C	A	7: 34,748,168	M8I	possibly damaging	Het
Clec4n	A	G	6: 123,235,516	E67G	probably benign	Het
Cobll1	A	T	2: 65,099,136	D653E	probably damaging	Het
Col9a1	T	C	1: 24,237,498		probably null	Het
Crip2	T	C	12: 113,143,504	L30P	probably damaging	Het
Ctbp1	C	T	5: 33,261,063	V22I	probably benign	Het
Cwc22	T	C	2: 77,917,177		probably benign	Het
Cyp4a32	C	A	4: 115,602,950	Y119*	probably null	Het
Dido1	G	T	2: 180,671,470	A463E	possibly damaging	Het
Dnah7a	G	A	1: 53,528,797	P1880L	probably benign	Het
Dock2	T	A	11: 34,239,705	T1489S	probably benign	Het
Dsp	A	G	13: 38,191,931	T1231A	probably damaging	Het
Eif2ak1	G	T	5: 143,873,899		probably benign	Het
Epc1	A	T	18: 6,452,360	M233K	probably damaging	Het
Fam189a2	G	A	19: 24,021,634	T140M	probably damaging	Het
Gigyf2	A	G	1: 87,443,638		probably benign	Het
Greb1	T	G	12: 16,707,851	H58P	probably damaging	Het
Gtpbp1	T	C	15: 79,713,448	I348T	possibly damaging	Het
Hck	A	T	2: 153,128,272	N64Y	probably benign	Het
Herc2	T	C	7: 56,168,996	S2812P	probably damaging	Het
Inpp4b	T	A	8: 81,952,834		probably null	Het
Kcnq5	A	C	1: 21,405,024	S473A	probably benign	Het
Lyst	A	G	13: 13,640,054	I1131M	possibly damaging	Het
Man2a2	T	C	7: 80,368,562	D160G	probably benign	Het
Marf1	C	T	16: 14,115,824	D1567N	probably benign	Het
Mars	T	C	10: 127,297,988	D680G	possibly damaging	Het
Mat1a	T	C	14: 41,121,840	S339P	probably damaging	Het
Megf8	T	C	7: 25,342,656	S1300P	probably damaging	Het
Mga	T	C	2: 119,902,698	L9S	probably damaging	Het
Mllt6	T	C	11: 97,672,451		probably benign	Het
Mrpl37	A	G	4: 107,064,495	L179P	probably benign	Het
Mtnr1a	G	T	8: 45,087,745	V248L	probably benign	Het
Mylk	T	C	16: 34,815,465	S19P	possibly damaging	Het
Olfr738	A	G	14: 50,414,401	T286A	probably damaging	Het
Parp8	A	T	13: 117,025,350		probably null	Het
Pcnx2	T	C	8: 125,752,284	D2075G	probably damaging	Het
Pigo	A	T	4: 43,021,460	I494K	probably benign	Het
Pkd1l1	A	T	11: 8,870,313	D1217E	probably benign	Het
Pkhd1l1	T	C	15: 44,505,644	V895A	probably benign	Het
Plcb4	A	T	2: 136,000,189	H1031L	possibly damaging	Het
Plxnb1	A	G	9: 109,108,921	K1245R	probably null	Het
Pold1	C	T	7: 44,542,757		probably benign	Het
Ptprq	T	C	10: 107,662,562	I885V	probably damaging	Het
Ptprz1	A	G	6: 23,050,474	D1398G	probably damaging	Het
Pygm	G	A	19: 6,389,887	A364T	probably benign	Het
Rbl1	T	C	2: 157,193,098	N354S	probably benign	Het
Scgb2b19	C	T	7: 33,279,612		probably null	Het
Slc26a8	C	T	17: 28,648,213	V545M	possibly damaging	Het
Slc27a1	T	A	8: 71,584,113		probably null	Het
Smpd1	A	G	7: 105,556,674	D416G	possibly damaging	Het
Sorbs3	A	G	14: 70,193,646	V284A	probably benign	Het
Stfa2l1	T	C	16: 36,161,784	V75A	probably damaging	Het
Syndig1	A	G	2: 149,930,921	D166G	probably damaging	Het
Tcp10a	G	A	17: 7,326,007		probably null	Het
Themis2	T	A	4: 132,782,901	I663F	possibly damaging	Het
Thrap3	T	C	4: 126,176,336	Q586R	probably damaging	Het
Tinag	C	A	9: 77,045,516	C62F	probably damaging	Het
Tmem206	A	G	1: 191,348,362		probably benign	Het
Tmod1	T	C	4: 46,090,884	Y146H	probably damaging	Het
Tmprss4	T	A	9: 45,184,385	I54F	possibly damaging	Het
Tnks	A	C	8: 34,834,603		probably benign	Het
Trim43a	GATTTATTTATTTATTTATTTATTTATTTATTTATTTATT	GATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATT	9: 88,582,989		probably benign	Het
Trpc6	A	G	9: 8,680,537	E844G	probably benign	Het
Ubtd2	C	T	11: 32,516,125	R115W	probably damaging	Het
Ubxn6	T	C	17: 56,069,042	D373G	probably benign	Het
Upf1	T	A	8: 70,341,524	Q244L	probably benign	Het
Usp33	A	G	3: 152,368,634	I372M	probably damaging	Het
Usp34	A	G	11: 23,351,629	E351G	probably damaging	Het
Utrn	A	G	10: 12,678,574		probably benign	Het
Vmn1r78	A	G	7: 12,152,581	K40E	possibly damaging	Het
Vmn2r7	T	A	3: 64,724,802	M80L	probably benign	Het
Vps13a	G	T	19: 16,701,238	Y1126*	probably null	Het
Wfdc11	T	C	2: 164,664,446	N60S	probably benign	Het
Wnk2	C	T	13: 49,071,110	D992N	probably damaging	Het
Zpbp2	C	A	11: 98,553,844	T66K	probably damaging	Het

Other mutations in Lrat

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL03206:Lrat	APN	3	82903349	missense	probably damaging	0.99
R1491:Lrat	UTSW	3	82903342	missense	probably benign	0.07
R1735:Lrat	UTSW	3	82897110	missense	probably benign	0.01
R2419:Lrat	UTSW	3	82903685	missense	probably damaging	1.00
R4446:Lrat	UTSW	3	82896986	missense	probably damaging	0.98
R5442:Lrat	UTSW	3	82903220	missense	probably damaging	1.00
R5495:Lrat	UTSW	3	82896982	missense	probably benign	0.00
R6255:Lrat	UTSW	3	82903505	missense	probably damaging	1.00
R6468:Lrat	UTSW	3	82903492	missense	probably damaging	1.00
R6909:Lrat	UTSW	3	82903654	missense	probably damaging	1.00
R7041:Lrat	UTSW	3	82903448	missense	probably benign	0.03
R7396:Lrat	UTSW	3	82903283	nonsense	probably null
R8369:Lrat	UTSW	3	82903558	missense	probably damaging	0.97
Z1177:Lrat	UTSW	3	82903490	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GAAATAGCCTTTCTGCGAGGCAAAC -3'
(R):5'- GGAAAACCGTGTCGCCCATCTAATG -3'

Sequencing Primer
(F):5'- GACTGATCCGAGAGCCATATCTG -3'
(R):5'- GCCCATCTAATGCCTGACATC -3'

Posted On

2014-03-14