Mutagenetix > Incidental Mutation

Incidental Mutation 'R5574:Letm1'

437100

Institutional Source

Beutler Lab

Gene Symbol

Letm1

Ensembl Gene

ENSMUSG00000005299

Gene Name

leucine zipper-EF-hand containing transmembrane protein 1

Synonyms

MMRRC Submission

043129-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.961) question?

Stock #

R5574 (G1)

Quality Score

199

Status

Validated

Chromosome

Chromosomal Location

33897017-33940061 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 33926730 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Methionine at position 189 (T189M)

Ref Sequence

ENSEMBL: ENSMUSP00000005431 (fasta)

Gene Model

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

AlphaFold

Q9Z2I0

Predicted Effect

possibly damaging
Transcript: ENSMUST00000005431
AA Change: T189M

PolyPhen 2 Score 0.458 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000005431
Gene: ENSMUSG00000005299
AA Change: T189M

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

0.1795

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.7%
20x: 96.6%

Validation Efficiency

99% (68/69)

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700129C05Rik	T	A	14: 59,380,205 (GRCm39)	N31I	possibly damaging	Het
Acvr1b	T	A	15: 101,099,958 (GRCm39)	M304K	probably benign	Het
Adamts1	G	T	16: 85,596,530 (GRCm39)	D106E	probably damaging	Het
Atosa	A	T	9: 74,917,672 (GRCm39)	D757V	probably damaging	Het
Blm	C	A	7: 80,149,521 (GRCm39)	C696F	probably damaging	Het
Bnip3l-ps	T	A	12: 18,267,119 (GRCm39)		noncoding transcript	Het
Ccdc171	A	T	4: 83,611,990 (GRCm39)	N895I	probably damaging	Het
Cdhr4	A	T	9: 107,870,527 (GRCm39)		probably benign	Het
Cfap97	T	C	8: 46,623,179 (GRCm39)	S190P	probably damaging	Het
Chrnb1	A	C	11: 69,684,509 (GRCm39)		probably benign	Het
Clns1a	A	G	7: 97,370,165 (GRCm39)		probably benign	Het
Col8a2	G	A	4: 126,205,061 (GRCm39)		probably benign	Het
Cr2	T	A	1: 194,823,544 (GRCm39)	E721V	probably damaging	Het
Csk	A	G	9: 57,536,584 (GRCm39)	V172A	probably benign	Het
Cyp2g1	G	A	7: 26,520,165 (GRCm39)	V466M	possibly damaging	Het
Cyp4f13	A	G	17: 33,148,179 (GRCm39)	Y349H	probably benign	Het
Dnm1l	T	C	16: 16,147,685 (GRCm39)	Y205C	probably damaging	Het
Dync1i2	A	T	2: 71,063,994 (GRCm39)	T113S	probably benign	Het
Edem2	T	C	2: 155,558,075 (GRCm39)	E186G	probably damaging	Het
Eya2	G	A	2: 165,605,736 (GRCm39)	R380H	probably damaging	Het
Gldn	A	G	9: 54,220,206 (GRCm39)	T132A	probably damaging	Het
Gm13941	A	T	2: 110,930,951 (GRCm39)	I74K	unknown	Het
Gm3898	C	T	9: 43,741,339 (GRCm39)		noncoding transcript	Het
Ighmbp2	C	T	19: 3,321,536 (GRCm39)	V408I	probably benign	Het
Klhdc10	C	T	6: 30,439,864 (GRCm39)	L127F	possibly damaging	Het
Lrrc17	A	T	5: 21,775,355 (GRCm39)	I306F	possibly damaging	Het
Lrrk2	T	A	15: 91,671,219 (GRCm39)	V2000E	probably damaging	Het
Mettl9	A	T	7: 120,647,093 (GRCm39)	E66D	probably benign	Het
Mroh1	T	A	15: 76,318,131 (GRCm39)	V877D	probably benign	Het
Mycbp2	C	T	14: 103,380,203 (GRCm39)	V3760M	possibly damaging	Het
Nos3	A	G	5: 24,573,859 (GRCm39)	T208A	possibly damaging	Het
Npdc1	G	A	2: 25,298,957 (GRCm39)	D284N	probably damaging	Het
Obp2a	A	T	2: 25,590,842 (GRCm39)	T70S	possibly damaging	Het
Or4a72	C	T	2: 89,405,321 (GRCm39)	V250I	possibly damaging	Het
Or52a5b	T	G	7: 103,417,323 (GRCm39)	I94L	possibly damaging	Het
Or5al6	T	C	2: 85,976,535 (GRCm39)	D181G	probably damaging	Het
Or8b8	A	T	9: 37,808,877 (GRCm39)	Y59F	probably damaging	Het
Or8h10	A	G	2: 86,808,867 (GRCm39)	V91A	probably benign	Het
Pate2	A	G	9: 35,597,411 (GRCm39)		probably benign	Het
Pdzph1	A	G	17: 59,280,942 (GRCm39)	F447L	probably benign	Het
Pias1	A	G	9: 62,827,775 (GRCm39)	C211R	probably damaging	Het
Plb1	A	G	5: 32,487,291 (GRCm39)	S929G	probably benign	Het
Pramel32	T	G	4: 88,546,280 (GRCm39)	E354A	probably benign	Het
Prc1	G	A	7: 79,944,290 (GRCm39)		probably benign	Het
Prex2	A	G	1: 11,210,282 (GRCm39)	D574G	probably damaging	Het
Rapgef4	G	A	2: 71,864,464 (GRCm39)		probably null	Het
Rmc1	CTGTGTGTT	CTGTGTGTTGTGTGTT	18: 12,318,063 (GRCm39)		probably null	Het
Rock2	T	C	12: 17,011,642 (GRCm39)	M690T	possibly damaging	Het
Sinhcaf	C	T	6: 148,846,378 (GRCm39)		probably benign	Het
Slc18a2	A	G	19: 59,249,837 (GRCm39)	I25V	probably benign	Het
Slc9a5	T	A	8: 106,091,323 (GRCm39)	I701K	probably benign	Het
Sorcs1	T	A	19: 50,210,571 (GRCm39)	N765Y	probably damaging	Het
Ssh2	A	T	11: 77,340,941 (GRCm39)	I698L	probably benign	Het
Stam	A	G	2: 14,120,675 (GRCm39)	D58G	probably damaging	Het
Thsd4	C	A	9: 59,879,683 (GRCm39)	R1018L	probably damaging	Het
Tnxb	A	G	17: 34,929,998 (GRCm39)	T2911A	probably benign	Het
Trpm7	A	C	2: 126,654,950 (GRCm39)	F1329L	probably benign	Het
Ttll9	A	G	2: 152,826,168 (GRCm39)	E126G	possibly damaging	Het
Tubgcp5	G	A	7: 55,455,077 (GRCm39)	V258M	probably benign	Het
Unc45a	G	A	7: 79,984,604 (GRCm39)	A232V	probably damaging	Het
Utp14b	G	A	1: 78,644,126 (GRCm39)	V675M	probably damaging	Het
Vmn2r67	T	A	7: 84,801,099 (GRCm39)	H279L	probably benign	Het
Vmn2r75	G	T	7: 85,815,510 (GRCm39)	A118E	probably benign	Het
Wdr36	A	T	18: 32,999,012 (GRCm39)	Q886L	probably damaging	Het
Zfp433	T	A	10: 81,555,125 (GRCm39)	Y27*	probably null	Het
Zfp715	A	T	7: 42,960,463 (GRCm39)	S43T	possibly damaging	Het
Zfyve26	A	G	12: 79,286,698 (GRCm39)	S2297P	possibly 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
R2145: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
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'- CTGCAGGAAATCACCAACGG -3'
(R):5'- CTGTGATAGAGAAGTCCCTTAAGTC -3'

Sequencing Primer
(F):5'- TCACCAACGGAGGAGACAGTG -3'
(R):5'- GTCCCTTAAGTCCTTAAAAGACAAG -3'

Posted On

2016-10-26