Mutagenetix > Incidental Mutation

Incidental Mutation 'R2145:Letm1'

233716

Institutional Source

Beutler Lab

Gene Symbol

Letm1

Ensembl Gene

ENSMUSG00000005299

Gene Name

leucine zipper-EF-hand containing transmembrane protein 1

Synonyms

MMRRC Submission

040148-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.961) question?

Stock #

R2145 (G1)

Quality Score

217

Status

Validated

Chromosome

Chromosomal Location

33897017-33940061 bp(-) (GRCm39)

Type of Mutation

frame shift

DNA Base Change (assembly)

A to AG at 33926859 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000005431 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000005431]

AlphaFold

Q9Z2I0

Predicted Effect

probably null
Transcript: ENSMUST00000005431

SMART Domains

Protein: ENSMUSP00000005431
Gene: ENSMUSG00000005299

Domain	Start	End	E-Value	Type
low complexity region	10	30	N/A	INTRINSIC
low complexity region	120	135	N/A	INTRINSIC
Pfam:LETM1	152	417	1.2e-111	PFAM
coiled coil region	445	493	N/A	INTRINSIC
low complexity region	503	513	N/A	INTRINSIC
coiled coil region	537	598	N/A	INTRINSIC
SCOP:d1c7va_	647	691	4e-3	SMART
coiled coil region	708	738	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144071

Predicted Effect

probably benign
Transcript: ENSMUST00000200827

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201981

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.5%
20x: 95.6%

Validation Efficiency

97% (101/104)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is localized to the inner mitochondrial membrane. The protein functions to maintain the mitochondrial tubular shapes and is required for normal mitochondrial morphology and cellular viability. Mutations in this gene cause Wolf-Hirschhorn syndrome, a complex malformation syndrome caused by the deletion of parts of the distal short arm of chromosome 4. Related pseudogenes have been identified on chromosomes 8, 15 and 19. [provided by RefSeq, Oct 2009]
PHENOTYPE: Homozygous deletion of this gene causes embryonic lethality prior to E6.5 while ~50% of heterozygotes die before E13.5. Surviving heterozygous mice show altered glucose metabolism, impaired control of brain ATP levels, and increased susceptibility to kainic acid-induced seizures. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 104 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca15	A	G	7: 119,953,701 (GRCm39)	N535S	probably benign	Het
Abcc6	A	T	7: 45,648,165 (GRCm39)	L717Q	probably benign	Het
Abraxas2	C	A	7: 132,484,790 (GRCm39)	Q278K	probably benign	Het
Acap2	A	T	16: 30,924,342 (GRCm39)	D637E	probably benign	Het
AI661453	A	G	17: 47,777,023 (GRCm39)		probably benign	Het
Aoah	A	T	13: 21,024,266 (GRCm39)	E74V	probably damaging	Het
Aoc1l1	A	T	6: 48,953,629 (GRCm39)	D518V	probably damaging	Het
Appl1	A	G	14: 26,671,576 (GRCm39)	L292S	possibly damaging	Het
Astl	T	A	2: 127,189,109 (GRCm39)	V166E	probably damaging	Het
Bbs1	T	G	19: 4,953,735 (GRCm39)	K143Q	possibly damaging	Het
Bbx	T	C	16: 50,094,907 (GRCm39)		probably benign	Het
Birc6	A	T	17: 74,967,408 (GRCm39)	Q4103L	possibly damaging	Het
C1qtnf2	T	G	11: 43,381,811 (GRCm39)	F178V	probably damaging	Het
Camta2	A	G	11: 70,562,401 (GRCm39)	F999L	probably benign	Het
Cfap68	T	C	9: 50,676,174 (GRCm39)	Y32C	probably damaging	Het
Clcn7	A	G	17: 25,363,425 (GRCm39)	I34V	probably benign	Het
Cntn5	G	T	9: 9,748,420 (GRCm39)	P487Q	probably damaging	Het
Ctu2	T	A	8: 123,205,891 (GRCm39)	I213K	probably benign	Het
Des	C	A	1: 75,340,108 (GRCm39)		probably benign	Het
Dgcr8	A	T	16: 18,098,094 (GRCm39)	D432E	probably benign	Het
Dlgap5	G	A	14: 47,633,380 (GRCm39)	R549*	probably null	Het
Dmac2l	A	G	12: 69,787,828 (GRCm39)	Q88R	probably damaging	Het
Dmxl2	T	C	9: 54,323,194 (GRCm39)	T1397A	probably damaging	Het
Dnmt1	T	A	9: 20,848,451 (GRCm39)		probably benign	Het
Dstyk	T	A	1: 132,391,113 (GRCm39)	M838K	probably damaging	Het
Dtwd1	C	A	2: 126,001,904 (GRCm39)	T208N	probably damaging	Het
Dvl1	G	A	4: 155,932,273 (GRCm39)	V28I	possibly damaging	Het
Dync1i2	T	A	2: 71,044,907 (GRCm39)		probably benign	Het
Fer1l6	T	A	15: 58,499,383 (GRCm39)	M1251K	probably benign	Het
Fmod	T	C	1: 133,968,256 (GRCm39)	Y99H	probably benign	Het
Fn1	A	T	1: 71,645,163 (GRCm39)	V1552D	probably damaging	Het
Fnip2	A	T	3: 79,407,739 (GRCm39)	S281T	probably damaging	Het
Glb1	A	G	9: 114,293,233 (GRCm39)	H536R	probably benign	Het
Glis2	T	A	16: 4,431,506 (GRCm39)	S344R	possibly damaging	Het
Gm4847	A	T	1: 166,462,472 (GRCm39)	S339R	probably benign	Het
Gpr155	A	G	2: 73,187,002 (GRCm39)	S44P	probably benign	Het
Gprin1	G	A	13: 54,886,445 (GRCm39)	P610S	probably damaging	Het
Gvin3	T	A	7: 106,202,215 (GRCm39)	H343L	possibly damaging	Het
H2-Ob	A	T	17: 34,461,554 (GRCm39)	M98L	probably benign	Het
H3c6	T	C	13: 23,746,530 (GRCm39)	T4A	probably benign	Het
Hmcn2	T	C	2: 31,223,943 (GRCm39)		probably benign	Het
Ikbke	C	A	1: 131,201,211 (GRCm39)	V176L	probably damaging	Het
Il13	T	C	11: 53,523,351 (GRCm39)	T85A	possibly damaging	Het
Inpp5k	A	T	11: 75,538,017 (GRCm39)		probably null	Het
Irgm2	T	C	11: 58,111,355 (GRCm39)	S361P	possibly damaging	Het
Itga11	C	T	9: 62,639,486 (GRCm39)		probably benign	Het
Kalrn	G	T	16: 33,829,632 (GRCm39)		probably benign	Het
Kcng1	C	A	2: 168,110,952 (GRCm39)	G71C	probably damaging	Het
Kcnq5	T	A	1: 21,575,573 (GRCm39)	D291V	probably damaging	Het
Klhl7	A	T	5: 24,305,861 (GRCm39)	M37L	probably benign	Het
Lhx6	C	T	2: 35,977,478 (GRCm39)	V325I	probably benign	Het
Lipc	A	G	9: 70,841,817 (GRCm39)	I9T	possibly damaging	Het
Lsmem1	GTACATACATACATACATACATACATACA	GTACATACATACATACATACATACATACATACA	12: 40,235,260 (GRCm39)		probably null	Het
Mast1	C	A	8: 85,648,107 (GRCm39)	G458V	probably damaging	Het
Mga	T	C	2: 119,794,638 (GRCm39)	V2565A	possibly damaging	Het
Mpzl2	C	G	9: 44,955,471 (GRCm39)	D127E	probably benign	Het
Mrtfb	T	C	16: 13,230,450 (GRCm39)	I1045T	probably damaging	Het
Myh3	T	A	11: 66,981,882 (GRCm39)	C793S	probably benign	Het
Nomo1	T	C	7: 45,715,928 (GRCm39)	L765P	probably damaging	Het
Nup210	A	G	6: 91,005,858 (GRCm39)	I1335T	possibly damaging	Het
Or52b3	T	C	7: 102,204,267 (GRCm39)		probably null	Het
Oxr1	T	A	15: 41,683,340 (GRCm39)	S254R	probably damaging	Het
Pan3	A	G	5: 147,466,908 (GRCm39)	I592V	possibly damaging	Het
Pask	C	T	1: 93,249,019 (GRCm39)	A794T	probably benign	Het
Pex2	T	C	3: 5,626,650 (GRCm39)	E53G	probably damaging	Het
Pfkfb2	T	C	1: 130,626,460 (GRCm39)	T438A	probably benign	Het
Phactr4	T	C	4: 132,098,095 (GRCm39)	E391G	probably damaging	Het
Pira2	A	T	7: 3,847,344 (GRCm39)	L115Q	probably damaging	Het
Pkhd1l1	A	T	15: 44,376,273 (GRCm39)		probably null	Het
Pnlip	A	G	19: 58,664,876 (GRCm39)	S235G	probably benign	Het
Prkd1	A	G	12: 50,536,694 (GRCm39)	V130A	possibly damaging	Het
Ptpn13	A	G	5: 103,703,999 (GRCm39)	T1344A	probably benign	Het
Ptprc	T	C	1: 138,001,419 (GRCm39)	Y780C	probably damaging	Het
Pxn	T	A	5: 115,690,815 (GRCm39)		probably benign	Het
Rap1gap2	G	A	11: 74,316,802 (GRCm39)	T245M	probably damaging	Het
Rc3h1	G	T	1: 160,757,827 (GRCm39)	K48N	probably damaging	Het
Rfwd3	T	C	8: 112,009,245 (GRCm39)	I444V	probably benign	Het
Rictor	C	T	15: 6,794,588 (GRCm39)	R293C	probably damaging	Het
Rif1	T	A	2: 52,001,412 (GRCm39)	I1622N	possibly damaging	Het
Rnf213	T	C	11: 119,306,019 (GRCm39)	V609A	probably benign	Het
Scgb1b2	G	T	7: 30,991,188 (GRCm39)		probably benign	Het
Serac1	A	T	17: 6,101,060 (GRCm39)	I448N	probably damaging	Het
Sh3kbp1	C	A	X: 158,607,492 (GRCm39)	T200K	probably benign	Het
Sned1	T	A	1: 93,199,406 (GRCm39)	F495L	probably damaging	Het
Socs7	T	C	11: 97,263,950 (GRCm39)	F281L	probably benign	Het
Spta1	C	T	1: 174,040,180 (GRCm39)	L1214F	probably benign	Het
Ssu72	A	G	4: 155,789,900 (GRCm39)	E21G	probably damaging	Het
Syngr4	A	G	7: 45,536,464 (GRCm39)	V186A	probably benign	Het
Tars3	G	A	7: 65,305,539 (GRCm39)	M254I	possibly damaging	Het
Tmem130	C	A	5: 144,680,595 (GRCm39)	V270L	probably benign	Het
Trim66	A	T	7: 109,074,320 (GRCm39)	I647N	probably damaging	Het
Tspyl2	A	T	X: 151,121,890 (GRCm39)	D572E	probably benign	Het
Unc45b	G	A	11: 82,808,580 (GRCm39)	R222H	probably benign	Het
Uxs1	T	C	1: 43,866,783 (GRCm39)	Y29C	probably damaging	Het
Virma	T	A	4: 11,548,726 (GRCm39)		probably benign	Het
Vmn1r202	C	T	13: 22,685,953 (GRCm39)	G155S	possibly damaging	Het
Vmn2r24	T	A	6: 123,755,972 (GRCm39)	F15I	probably benign	Het
Wdr64	A	G	1: 175,594,661 (GRCm39)	T471A	probably benign	Het
Zfa-ps	T	A	10: 52,419,373 (GRCm39)		noncoding transcript	Het
Zfp260	A	G	7: 29,804,765 (GRCm39)	K222E	probably damaging	Het
Zfp300	A	G	X: 20,948,190 (GRCm39)	S525P	possibly damaging	Het
Zfp821	A	G	8: 110,450,979 (GRCm39)	D324G	probably damaging	Het
Zfp934	T	C	13: 62,665,648 (GRCm39)	D331G	probably damaging	Het
Zscan29	T	C	2: 121,000,587 (GRCm39)	R7G	probably damaging	Het

Other mutations in Letm1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01013:Letm1	APN	5	33,919,934 (GRCm39)	missense	possibly damaging	0.82
IGL01073:Letm1	APN	5	33,906,144 (GRCm39)	missense	possibly damaging	0.89
IGL01882:Letm1	APN	5	33,927,009 (GRCm39)	missense	probably benign	0.00
IGL02186:Letm1	APN	5	33,902,391 (GRCm39)	missense	probably benign	0.00
IGL02699:Letm1	APN	5	33,902,492 (GRCm39)	missense	possibly damaging	0.93
IGL03089:Letm1	APN	5	33,918,202 (GRCm39)	missense	probably damaging	1.00
R0466:Letm1	UTSW	5	33,919,074 (GRCm39)	splice site	probably benign
R0639:Letm1	UTSW	5	33,926,770 (GRCm39)	missense	possibly damaging	0.88
R1370:Letm1	UTSW	5	33,936,026 (GRCm39)	splice site	probably null
R1415:Letm1	UTSW	5	33,926,906 (GRCm39)	missense	probably benign	0.06
R1511:Letm1	UTSW	5	33,909,899 (GRCm39)	missense	probably damaging	1.00
R1714:Letm1	UTSW	5	33,918,228 (GRCm39)	missense	possibly damaging	0.51
R1771:Letm1	UTSW	5	33,926,811 (GRCm39)	missense	probably damaging	1.00
R1990:Letm1	UTSW	5	33,926,859 (GRCm39)	frame shift	probably null
R1991:Letm1	UTSW	5	33,926,859 (GRCm39)	frame shift	probably null
R2143:Letm1	UTSW	5	33,926,859 (GRCm39)	frame shift	probably null
R2202:Letm1	UTSW	5	33,926,830 (GRCm39)	missense	possibly damaging	0.64
R2290:Letm1	UTSW	5	33,926,859 (GRCm39)	frame shift	probably null
R2292:Letm1	UTSW	5	33,926,859 (GRCm39)	frame shift	probably null
R5574:Letm1	UTSW	5	33,926,730 (GRCm39)	missense	possibly damaging	0.46
R6954:Letm1	UTSW	5	33,939,851 (GRCm39)	missense	probably benign	0.35
R7265:Letm1	UTSW	5	33,935,992 (GRCm39)	missense	possibly damaging	0.62
R8713:Letm1	UTSW	5	33,919,849 (GRCm39)	missense	probably damaging	1.00
R9028:Letm1	UTSW	5	33,909,847 (GRCm39)	missense	probably damaging	1.00
R9061:Letm1	UTSW	5	33,918,213 (GRCm39)	missense	probably damaging	1.00
R9420:Letm1	UTSW	5	33,926,802 (GRCm39)	missense	probably damaging	1.00
S24628:Letm1	UTSW	5	33,904,790 (GRCm39)	missense	probably benign
S24628:Letm1	UTSW	5	33,904,788 (GRCm39)	missense	probably benign	0.00
X0066:Letm1	UTSW	5	33,919,915 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ACTGACGTTTTATCCAGAGGAG -3'
(R):5'- AACATGGACACCTGCCTCTG -3'

Sequencing Primer
(F):5'- CGTTTTATCCAGAGGAGTAGAGC -3'
(R):5'- CTCTGCAAGGCTGGTGGTTAC -3'

Posted On

2014-10-01