Mutagenetix > Incidental Mutation

Incidental Mutation 'R1771:Letm1'

196569

Institutional Source

Beutler Lab

Gene Symbol

Letm1

Ensembl Gene

ENSMUSG00000005299

Gene Name

leucine zipper-EF-hand containing transmembrane protein 1

Synonyms

MMRRC Submission

039802-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.958) question?

Stock #

R1771 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

33739673-33782817 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 33769467 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Leucine at position 162 (H162L)

Ref Sequence

ENSEMBL: ENSMUSP00000005431 (fasta)

Gene Model

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

AlphaFold

Q9Z2I0

Predicted Effect

probably damaging
Transcript: ENSMUST00000005431
AA Change: H162L

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

SMART Domains

Protein: ENSMUSP00000005431
Gene: ENSMUSG00000005299
AA Change: H162L

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

Coding Region Coverage

1x: 97.4%
3x: 96.9%
10x: 95.2%
20x: 92.0%

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 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: 102 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acss3	A	G	10: 106,937,200	S642P	probably damaging	Het
Adam30	T	C	3: 98,161,519	S95P	possibly damaging	Het
Ahnak	G	A	19: 9,013,753	V4134I	probably benign	Het
AI314180	A	G	4: 58,879,100	I63T	probably damaging	Het
Ankrd13a	T	C	5: 114,803,588	V512A	probably benign	Het
Asph	A	T	4: 9,598,773	S149R	probably damaging	Het
Atp2b4	C	A	1: 133,732,393	V384L	probably damaging	Het
Atp8a1	A	G	5: 67,647,731	W1014R	probably damaging	Het
Cand1	A	C	10: 119,208,306	N1054K	probably benign	Het
Car15	A	T	16: 17,836,866	V96E	probably damaging	Het
Ccdc129	T	C	6: 55,898,147	S361P	probably benign	Het
Cd1d1	T	C	3: 86,998,665	E101G	possibly damaging	Het
Cd84	A	G	1: 171,872,750	T145A	possibly damaging	Het
Ceacam1	T	A	7: 25,472,044	T332S	probably benign	Het
Clca2	A	T	3: 145,081,410	V500E	probably benign	Het
Cul9	A	T	17: 46,537,812	M666K	probably benign	Het
Dennd3	A	G	15: 73,555,101	T776A	possibly damaging	Het
Dennd5a	T	C	7: 109,918,686	D581G	probably damaging	Het
Dgkh	A	G	14: 78,609,527	V371A	probably damaging	Het
Dhcr24	A	G	4: 106,578,253	T314A	probably benign	Het
Diaph1	G	T	18: 37,891,018	P589Q	unknown	Het
Disp2	C	T	2: 118,791,297	Q837*	probably null	Het
Dusp3	A	T	11: 101,984,735	M1K	probably null	Het
Epp13	G	T	7: 6,277,542		probably null	Het
Erich3	A	C	3: 154,748,472	D625A	possibly damaging	Het
Fat2	G	A	11: 55,310,865	S461L	probably benign	Het
Fmn2	A	G	1: 174,608,776		probably benign	Het
Foxi1	A	G	11: 34,207,594	Y144H	probably damaging	Het
Ftcd	G	A	10: 76,587,368	V458M	probably damaging	Het
Gm3604	C	A	13: 62,370,074	G157*	probably null	Het
Gnpda1	C	T	18: 38,333,327	R79Q	probably benign	Het
Gpr65	T	A	12: 98,276,000	I304K	probably damaging	Het
Grem1	T	C	2: 113,749,676	E160G	probably benign	Het
Gria2	T	A	3: 80,692,301	K759*	probably null	Het
Gsg1l	A	G	7: 125,958,573	S128P	probably damaging	Het
Hdac1	A	T	4: 129,521,428	I240N	probably damaging	Het
Hic2	C	T	16: 17,258,714	T469M	probably benign	Het
Hoxc10	A	C	15: 102,967,087	D77A	probably damaging	Het
Klhl14	T	A	18: 21,651,620	H250L	probably damaging	Het
Klk1b24	A	G	7: 44,188,229		probably null	Het
Loxl3	A	T	6: 83,049,909	Y573F	probably damaging	Het
Macf1	A	T	4: 123,512,108	I330N	probably damaging	Het
Mchr1	T	A	15: 81,237,235	I62N	probably damaging	Het
Mcm8	C	T	2: 132,843,556	Q803*	probably null	Het
Msh3	T	G	13: 92,212,496	D1075A	probably benign	Het
Msh6	T	A	17: 87,984,522	V235D	probably benign	Het
Mthfd2l	A	T	5: 90,974,395	D253V	probably damaging	Het
Mtor	T	C	4: 148,470,624	V901A	possibly damaging	Het
Muc20	A	T	16: 32,793,852	I385N	probably damaging	Het
Myo6	G	T	9: 80,285,800	C829F	probably damaging	Het
Nbea	T	C	3: 55,934,519	I1914V	probably benign	Het
Ncor1	T	C	11: 62,327,112	E1462G	probably damaging	Het
Necab1	A	G	4: 15,111,267	Y54H	probably damaging	Het
Nlrp4b	A	G	7: 10,718,593	K15R	probably damaging	Het
Ntrk1	A	G	3: 87,789,630	S139P	probably benign	Het
Oas1d	T	C	5: 120,915,837	F120S	probably damaging	Het
Ofd1	A	G	X: 166,406,006	Y755H	probably benign	Het
Olfr118	A	G	17: 37,672,663	I213M	probably damaging	Het
Olfr1317	T	G	2: 112,142,720	Y258*	probably null	Het
Olfr1412	A	G	1: 92,589,115	I262V	probably benign	Het
Olfr368	T	A	2: 37,332,418	F224I	probably benign	Het
Olfr482	A	C	7: 108,095,609		probably null	Het
Olfr539	A	G	7: 140,668,135	T276A	probably benign	Het
Plekha6	T	C	1: 133,273,913	S355P	probably benign	Het
Prdm14	T	C	1: 13,118,858	K421E	probably damaging	Het
Prss36	A	G	7: 127,933,453	L731P	probably damaging	Het
Rad51d	A	G	11: 82,883,938	L97P	probably damaging	Het
Rbl1	C	A	2: 157,163,534		probably null	Het
Rnh1	G	T	7: 141,164,606	A52D	possibly damaging	Het
Rps24	A	G	14: 24,491,762	T6A	probably damaging	Het
Ryr2	A	C	13: 11,745,176		probably null	Het
Samd4	A	T	14: 47,089,075	N454I	probably damaging	Het
Sap130	T	C	18: 31,636,082	I32T	probably benign	Het
Sap30l	A	T	11: 57,806,099	N85I	probably damaging	Het
Sbf2	G	A	7: 110,461,146	Q204*	probably null	Het
Slc45a3	T	C	1: 131,976,956	W6R	possibly damaging	Het
Snx16	A	G	3: 10,419,161	V334A	probably damaging	Het
Soat1	C	T	1: 156,442,421	V143I	probably benign	Het
Sp8	T	A	12: 118,849,567	F386I	probably damaging	Het
Spag6	C	T	2: 18,734,117	S286L	probably benign	Het
Srpr	A	T	9: 35,212,851	N31I	possibly damaging	Het
Ssbp4	A	G	8: 70,598,852		probably null	Het
Stxbp2	G	T	8: 3,634,064	A124S	probably benign	Het
Tacc2	A	G	7: 130,742,240	K700R	probably damaging	Het
Tatdn2	A	T	6: 113,702,099		probably null	Het
Tecrl	G	A	5: 83,291,287	T226I	probably damaging	Het
Timeless	T	G	10: 128,247,608	V702G	probably benign	Het
Tjp1	A	T	7: 65,313,005	S1061R	probably benign	Het
Tmem39b	A	T	4: 129,693,218	C67S	probably damaging	Het
Tstd3	T	C	4: 21,759,475	Y99C	probably damaging	Het
Ttc39c	T	A	18: 12,684,824		probably null	Het
Ttll7	C	T	3: 146,894,405	P23S	probably benign	Het
Uba5	A	G	9: 104,049,908	F290S	probably damaging	Het
Ubap2l	T	C	3: 90,019,231	Y623C	probably damaging	Het
Ube3a	A	G	7: 59,275,966	E164G	probably damaging	Het
Ugcg	A	G	4: 59,207,775	N38S	probably benign	Het
Ugp2	G	A	11: 21,329,915	T283I	probably damaging	Het
Vmn1r55	A	T	7: 5,146,920	I168N	probably benign	Het
Wdr27	A	C	17: 14,892,441	S668A	probably damaging	Het
Wnt2	T	A	6: 18,008,697	N247I	probably damaging	Het
Zfp850	A	T	7: 27,985,275	C15*	probably null	Het
Zfp959	A	G	17: 55,897,677		probably null	Het

Other mutations in Letm1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01013:Letm1	APN	5	33762590	missense	possibly damaging	0.82
IGL01073:Letm1	APN	5	33748800	missense	possibly damaging	0.89
IGL01882:Letm1	APN	5	33769665	missense	probably benign	0.00
IGL02186:Letm1	APN	5	33745047	missense	probably benign	0.00
IGL02699:Letm1	APN	5	33745148	missense	possibly damaging	0.93
IGL03089:Letm1	APN	5	33760858	missense	probably damaging	1.00
R0466:Letm1	UTSW	5	33761730	splice site	probably benign
R0639:Letm1	UTSW	5	33769426	missense	possibly damaging	0.88
R1370:Letm1	UTSW	5	33778682	splice site	probably null
R1415:Letm1	UTSW	5	33769562	missense	probably benign	0.06
R1511:Letm1	UTSW	5	33752555	missense	probably damaging	1.00
R1714:Letm1	UTSW	5	33760884	missense	possibly damaging	0.51
R1990:Letm1	UTSW	5	33769515	frame shift	probably null
R1991:Letm1	UTSW	5	33769515	frame shift	probably null
R2143:Letm1	UTSW	5	33769515	frame shift	probably null
R2145:Letm1	UTSW	5	33769515	frame shift	probably null
R2202:Letm1	UTSW	5	33769486	missense	possibly damaging	0.64
R2290:Letm1	UTSW	5	33769515	frame shift	probably null
R2292:Letm1	UTSW	5	33769515	frame shift	probably null
R5574:Letm1	UTSW	5	33769386	missense	possibly damaging	0.46
R6954:Letm1	UTSW	5	33782507	missense	probably benign	0.35
R7265:Letm1	UTSW	5	33778648	missense	possibly damaging	0.62
R8713:Letm1	UTSW	5	33762505	missense	probably damaging	1.00
R9028:Letm1	UTSW	5	33752503	missense	probably damaging	1.00
R9061:Letm1	UTSW	5	33760869	missense	probably damaging	1.00
R9420:Letm1	UTSW	5	33769458	missense	probably damaging	1.00
S24628:Letm1	UTSW	5	33747444	missense	probably benign	0.00
S24628:Letm1	UTSW	5	33747446	missense	probably benign
X0066:Letm1	UTSW	5	33762571	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGTCAGCACTGGCATGACAACTC -3'
(R):5'- AACATGGACACCTGCCTCTGCAAG -3'

Sequencing Primer
(F):5'- ACTCACTTGTAGCATGAGCTAGG -3'
(R):5'- TGGTTACGGGACCTCAGTACC -3'

Posted On

2014-05-23