Mutagenetix > Incidental Mutation

Incidental Mutation 'R1511:Letm1'

168297

Institutional Source

Beutler Lab

Gene Symbol

Letm1

Ensembl Gene

ENSMUSG00000005299

Gene Name

leucine zipper-EF-hand containing transmembrane protein 1

Synonyms

MMRRC Submission

039558-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.961) question?

Stock #

R1511 (G1)

Quality Score

211

Status

Not validated

Chromosome

Chromosomal Location

33897017-33940061 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 33909899 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Tryptophan at position 378 (C378W)

Ref Sequence

ENSEMBL: ENSMUSP00000005431 (fasta)

Gene Model

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

AlphaFold

Q9Z2I0

Predicted Effect

probably damaging
Transcript: ENSMUST00000005431
AA Change: C378W

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000005431
Gene: ENSMUSG00000005299
AA Change: C378W

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: ENSMUST00000149886

Coding Region Coverage

1x: 99.0%
3x: 98.0%
10x: 95.4%
20x: 89.7%

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: 105 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aacs	C	A	5: 125,592,041 (GRCm39)	N576K	probably benign	Het
Abca5	G	T	11: 110,190,804 (GRCm39)	L769M	probably damaging	Het
Abca5	T	A	11: 110,190,812 (GRCm39)	H766L	possibly damaging	Het
Acvr1c	A	G	2: 58,177,896 (GRCm39)	I191T	probably damaging	Het
Agps	A	T	2: 75,697,123 (GRCm39)	E314D	probably damaging	Het
Agxt	G	A	1: 93,063,490 (GRCm39)	G131R	probably damaging	Het
Ak8	A	G	2: 28,632,758 (GRCm39)	T326A	probably benign	Het
Aldoart2	T	A	12: 55,613,062 (GRCm39)	I329N	probably benign	Het
Apaf1	T	C	10: 90,896,047 (GRCm39)	I342V	possibly damaging	Het
Arhgap40	T	C	2: 158,369,081 (GRCm39)	S68P	probably benign	Het
Arsi	G	A	18: 61,049,723 (GRCm39)	G202E	probably benign	Het
AU022252	C	T	4: 119,085,294 (GRCm39)	R71Q	possibly damaging	Het
Baz1b	T	C	5: 135,246,636 (GRCm39)	L695P	probably damaging	Het
Baz2b	A	T	2: 59,792,368 (GRCm39)	S587T	probably benign	Het
Cep76	T	C	18: 67,758,028 (GRCm39)	M421V	probably benign	Het
Clk2	A	G	3: 89,076,010 (GRCm39)	D60G	probably damaging	Het
Clstn3	G	T	6: 124,439,128 (GRCm39)	T6K	probably damaging	Het
Cluap1	T	A	16: 3,737,422 (GRCm39)	D180E	probably benign	Het
Col12a1	T	C	9: 79,606,834 (GRCm39)	I530V	probably benign	Het
Cpt1a	T	C	19: 3,415,788 (GRCm39)		probably benign	Het
Cr2	T	G	1: 194,837,580 (GRCm39)	K797Q	possibly damaging	Het
Crybg3	C	A	16: 59,374,475 (GRCm39)	V2260L	probably benign	Het
Csnk1a1	T	A	18: 61,718,321 (GRCm39)		probably benign	Het
Cxcr1	T	C	1: 74,231,929 (GRCm39)	D31G	probably benign	Het
Cyp2a5	G	T	7: 26,535,361 (GRCm39)	D108Y	probably damaging	Het
Dnajc1	A	G	2: 18,227,538 (GRCm39)	V376A	possibly damaging	Het
Eif4enif1	T	C	11: 3,186,278 (GRCm39)	V462A	probably benign	Het
Elmo1	A	G	13: 20,474,647 (GRCm39)	K357R	possibly damaging	Het
Eml6	T	A	11: 29,768,374 (GRCm39)	H771L	probably damaging	Het
Epb41l4a	A	G	18: 33,965,717 (GRCm39)	I370T	probably benign	Het
Esp36	A	T	17: 38,728,172 (GRCm39)	N79K	possibly damaging	Het
Fam229b	A	G	10: 38,994,915 (GRCm39)	*81Q	probably null	Het
Fat4	T	C	3: 39,037,225 (GRCm39)	Y3626H	probably damaging	Het
Fbn1	A	T	2: 125,148,205 (GRCm39)	F2681Y	probably benign	Het
Gad1-ps	A	G	10: 99,281,331 (GRCm39)		noncoding transcript	Het
Galm	C	A	17: 80,490,696 (GRCm39)	N284K	probably damaging	Het
Gtf3c2	A	T	5: 31,316,446 (GRCm39)	S735T	probably benign	Het
Hsph1	A	T	5: 149,553,848 (GRCm39)	S207T	probably benign	Het
Il33	C	T	19: 29,932,615 (GRCm39)	R159C	probably damaging	Het
Invs	A	G	4: 48,382,148 (GRCm39)	N106S	possibly damaging	Het
Kif21b	G	T	1: 136,097,062 (GRCm39)		probably null	Het
Kirrel2	A	G	7: 30,155,923 (GRCm39)	C42R	probably damaging	Het
Lrrc71	T	A	3: 87,652,791 (GRCm39)	K160N	probably benign	Het
Lrrtm3	A	G	10: 63,924,804 (GRCm39)	I121T	probably damaging	Het
Lztr1	T	A	16: 17,327,534 (GRCm39)	V79E	probably damaging	Het
Mmp8	T	G	9: 7,566,279 (GRCm39)	D378E	probably damaging	Het
Mpzl3	A	G	9: 44,977,827 (GRCm39)	E145G	probably damaging	Het
Mrps2	C	T	2: 28,359,676 (GRCm39)	L178F	probably damaging	Het
Mzb1	A	G	18: 35,780,875 (GRCm39)		probably null	Het
Nckap1	T	C	2: 80,383,759 (GRCm39)	D135G	probably damaging	Het
Ndst1	A	G	18: 60,830,242 (GRCm39)	F623L	possibly damaging	Het
Nlrp5	A	T	7: 23,112,772 (GRCm39)	D143V	probably damaging	Het
Or14a260	T	C	7: 85,985,553 (GRCm39)	D17G	possibly damaging	Het
Or4a69	T	C	2: 89,312,592 (GRCm39)	M296V	probably null	Het
Or4b1d	A	G	2: 89,968,748 (GRCm39)	V245A	probably benign	Het
Or4c120	A	G	2: 89,001,281 (GRCm39)	S92P	probably damaging	Het
Or4f58	A	G	2: 111,851,749 (GRCm39)	V150A	probably benign	Het
Or52b4i	T	C	7: 102,191,332 (GRCm39)	L63P	probably damaging	Het
Or8b44	A	G	9: 38,410,114 (GRCm39)	I50V	probably benign	Het
Or8g17	T	C	9: 38,930,321 (GRCm39)	D172G	probably benign	Het
Parp14	T	G	16: 35,677,594 (GRCm39)	E791D	probably benign	Het
Pcdh8	C	T	14: 80,006,829 (GRCm39)	R578H	possibly damaging	Het
Phrf1	T	A	7: 140,839,714 (GRCm39)		probably benign	Het
Polr3b	C	A	10: 84,516,249 (GRCm39)	H626N	probably benign	Het
Ppp1r12a	A	G	10: 108,087,720 (GRCm39)	T58A	probably benign	Het
Ppp4r3b	T	A	11: 29,132,460 (GRCm39)	V33D	probably damaging	Het
Ppp5c	A	G	7: 16,743,907 (GRCm39)	Y176H	probably damaging	Het
R3hdm1	A	G	1: 128,124,742 (GRCm39)	Y343C	probably damaging	Het
Rabac1	C	T	7: 24,671,555 (GRCm39)	V122M	probably damaging	Het
Rasef	G	T	4: 73,653,985 (GRCm39)	Q561K	probably damaging	Het
Rbl1	A	G	2: 157,037,554 (GRCm39)	S198P	probably damaging	Het
Rbm12	A	T	2: 155,939,456 (GRCm39)	M272K	probably damaging	Het
Rexo1	T	G	10: 80,385,884 (GRCm39)	K391N	possibly damaging	Het
Rnf43	T	C	11: 87,622,173 (GRCm39)	S384P	probably benign	Het
Rpsa	A	T	9: 119,960,066 (GRCm39)	I210F	possibly damaging	Het
Rslcan18	A	G	13: 67,247,016 (GRCm39)	Y75H	possibly damaging	Het
Scn9a	T	A	2: 66,357,157 (GRCm39)	D1048V	probably benign	Het
Sec11a	T	C	7: 80,577,482 (GRCm39)		probably null	Het
Sidt2	A	G	9: 45,861,387 (GRCm39)	V19A	probably damaging	Het
Snx14	G	A	9: 88,280,417 (GRCm39)	Q522*	probably null	Het
Stx1b	A	G	7: 127,414,144 (GRCm39)	L74S	probably damaging	Het
Tm7sf3	A	T	6: 146,511,376 (GRCm39)	M371K	probably benign	Het
Tmem115	T	C	9: 107,412,174 (GRCm39)	V166A	probably benign	Het
Traf5	T	A	1: 191,731,912 (GRCm39)	T310S	probably benign	Het
Trdn	A	G	10: 33,342,448 (GRCm39)	K619E	probably benign	Het
Trmt10a	T	A	3: 137,857,945 (GRCm39)		probably null	Het
Txk	A	C	5: 72,865,014 (GRCm39)	I287R	probably damaging	Het
Txndc16	T	C	14: 45,389,344 (GRCm39)	D452G	probably damaging	Het
Ube2f	G	A	1: 91,190,023 (GRCm39)		probably null	Het
Ubtfl1	T	G	9: 18,321,489 (GRCm39)	I339R	probably benign	Het
Upf1	A	G	8: 70,791,155 (GRCm39)	I529T	probably damaging	Het
Vmn1r197	A	G	13: 22,512,823 (GRCm39)	D248G	possibly damaging	Het
Vmn1r5	A	T	6: 56,962,771 (GRCm39)	T149S	probably benign	Het
Vmn1r83	C	T	7: 12,055,197 (GRCm39)	V287I	possibly damaging	Het
Vmn2r118	G	A	17: 55,915,496 (GRCm39)	R485*	probably null	Het
Vmn2r130	A	G	17: 23,282,775 (GRCm39)	T152A	probably benign	Het
Vps13b	T	C	15: 35,840,121 (GRCm39)	F2448L	probably damaging	Het
Vps13b	A	G	15: 35,841,719 (GRCm39)	N2583S	probably benign	Het
Wscd1	C	T	11: 71,679,501 (GRCm39)	P458L	probably damaging	Het
Xylt2	T	A	11: 94,561,259 (GRCm39)	D168V	probably damaging	Het
Zdhhc2	A	G	8: 40,921,013 (GRCm39)	T306A	probably benign	Het
Zfp804b	A	T	5: 6,819,771 (GRCm39)	D1097E	possibly damaging	Het
Zfp93	T	A	7: 23,975,156 (GRCm39)	C380*	probably null	Het
Zfp960	T	A	17: 17,308,518 (GRCm39)	C411S	probably damaging	Het
Zmynd15	T	A	11: 70,355,619 (GRCm39)	V430E	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
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
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'- TGCTGGTCTGGAGCAAAGGTAGATG -3'
(R):5'- CCCTTAAGTCTCAAGGCACTGAGC -3'

Sequencing Primer
(F):5'- TGGAGCAAAGGTAGATGATTCCC -3'
(R):5'- ttctcctcttcctcctcctc -3'

Posted On

2014-04-13