Mutagenetix > Incidental Mutation

Incidental Mutation 'R9061:Letm1'

688969

Institutional Source

Beutler Lab

Gene Symbol

Letm1

Ensembl Gene

ENSMUSG00000005299

Gene Name

leucine zipper-EF-hand containing transmembrane protein 1

Synonyms

MMRRC Submission

068887-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.957) question?

Stock #

R9061 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

33739673-33782817 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 33760869 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 311 (F311L)

Ref Sequence

ENSEMBL: ENSMUSP00000005431 (fasta)

Gene Model

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

AlphaFold

Q9Z2I0

Predicted Effect

probably damaging
Transcript: ENSMUST00000005431
AA Change: F311L

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

SMART Domains

Protein: ENSMUSP00000005431
Gene: ENSMUSG00000005299
AA Change: F311L

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

probably benign
Transcript: ENSMUST00000200827

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (60/60)

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: 58 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930518I15Rik	A	G	2: 156,857,213 (GRCm38)	M1T	probably null	Het
Abca13	A	G	11: 9,277,847 (GRCm38)	E630G	probably benign	Het
Abcf2	T	A	5: 24,573,506 (GRCm38)	H218L	possibly damaging	Het
Abo	A	T	2: 26,843,383 (GRCm38)	M268K	probably benign	Het
Ankrd33	G	T	15: 101,116,148 (GRCm38)		probably benign	Het
Apc	G	C	18: 34,313,198 (GRCm38)	R1049T	probably damaging	Het
Atg16l2	T	C	7: 101,292,131 (GRCm38)	K412E	probably damaging	Het
Cachd1	G	A	4: 100,952,005 (GRCm38)		probably null	Het
Ccdc152	T	G	15: 3,301,161 (GRCm38)	K11Q	probably damaging	Het
Ccdc38	T	A	10: 93,565,873 (GRCm38)	W232R	probably damaging	Het
Cluh	C	T	11: 74,660,366 (GRCm38)	P347L	possibly damaging	Het
Cntn3	A	G	6: 102,337,327 (GRCm38)	L142P	probably damaging	Het
Ctnnd2	T	A	15: 30,806,738 (GRCm38)	M601K	probably damaging	Het
D930048N14Rik	G	A	11: 51,654,907 (GRCm38)	D209N	unknown	Het
Dcaf6	A	T	1: 165,336,763 (GRCm38)	N814K	probably damaging	Het
Dhx8	A	T	11: 101,741,580 (GRCm38)	D455V	possibly damaging	Het
Fcna	A	C	2: 25,624,944 (GRCm38)	L301W	possibly damaging	Het
Garin1b	C	T	6: 29,323,903 (GRCm38)	T209I	probably benign	Het
Gdf9	T	G	11: 53,433,442 (GRCm38)	C13G	probably damaging	Het
Hells	T	A	19: 38,945,414 (GRCm38)	N226K	probably damaging	Het
Hes6	A	G	1: 91,412,339 (GRCm38)	S132P	probably damaging	Het
Ifi207	A	T	1: 173,736,587 (GRCm38)		probably benign	Het
Ighv16-1	A	T	12: 114,068,884 (GRCm38)	Y99*	probably null	Het
Kirrel2	T	C	7: 30,450,880 (GRCm38)	I508V	probably benign	Het
Klhl38	T	A	15: 58,322,626 (GRCm38)	I236F	probably damaging	Het
Klk15	C	T	7: 43,938,366 (GRCm38)	H73Y	possibly damaging	Het
Lamc1	A	T	1: 153,251,124 (GRCm38)	C425*	probably null	Het
Lypd11	A	T	7: 24,722,748 (GRCm38)	I192N	possibly damaging	Het
Mapk8ip2	T	C	15: 89,457,813 (GRCm38)	V409A	possibly damaging	Het
Mybpc1	C	T	10: 88,555,639 (GRCm38)	C318Y	probably damaging	Het
Myo15a	A	G	11: 60,502,866 (GRCm38)	Y1141C		Het
Ndufv2	T	A	17: 66,083,480 (GRCm38)	D165V	probably damaging	Het
Nrde2	T	C	12: 100,143,864 (GRCm38)	K303E	probably benign	Het
Nup205	T	A	6: 35,219,873 (GRCm38)		probably benign	Het
Or1j12	A	G	2: 36,452,885 (GRCm38)	Q100R	probably damaging	Het
Or2f2	A	T	6: 42,790,207 (GRCm38)	H56L	probably damaging	Het
Or5b118	A	G	19: 13,471,159 (GRCm38)	N21S	probably damaging	Het
Otof	C	T	5: 30,388,657 (GRCm38)	V451I	possibly damaging	Het
Pask	G	A	1: 93,325,469 (GRCm38)	Q399*	probably null	Het
Pbk	T	A	14: 65,811,990 (GRCm38)	F39I	probably benign	Het
Pdzd2	T	C	15: 12,374,667 (GRCm38)	K1794R	possibly damaging	Het
Pibf1	T	C	14: 99,186,633 (GRCm38)		probably null	Het
Ppip5k2	G	A	1: 97,717,462 (GRCm38)	T1089I	probably damaging	Het
Ppp1cb	T	A	5: 32,478,148 (GRCm38)	F45L	possibly damaging	Het
Pramel21	T	G	4: 143,616,171 (GRCm38)	S283A	possibly damaging	Het
Samd4	T	C	14: 47,064,271 (GRCm38)	F344S	probably damaging	Het
Slc2a13	C	T	15: 91,350,130 (GRCm38)	M334I	possibly damaging	Het
Slc37a1	C	T	17: 31,337,391 (GRCm38)	A363V	probably damaging	Het
Slc8a3	T	A	12: 81,216,766 (GRCm38)	I616F	probably damaging	Het
Srcin1	A	G	11: 97,536,380 (GRCm38)	L257P	probably damaging	Het
Tarbp1	A	G	8: 126,447,141 (GRCm38)	F945L	probably damaging	Het
Thbs4	A	T	13: 92,774,679 (GRCm38)		probably null	Het
Tmco1	C	T	1: 167,308,563 (GRCm38)		probably benign	Het
Trim62	G	A	4: 128,909,170 (GRCm38)	V338M	probably damaging	Het
Ttll9	C	T	2: 152,976,193 (GRCm38)	H20Y	possibly damaging	Het
Uevld	A	T	7: 46,938,058 (GRCm38)	I298N	probably damaging	Het
Zan	T	C	5: 137,464,391 (GRCm38)	E842G	probably damaging	Het
Zdbf2	T	G	1: 63,307,137 (GRCm38)	S1558R		Het

Other mutations in Letm1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01013:Letm1	APN	5	33,762,590 (GRCm38)	missense	possibly damaging	0.82
IGL01073:Letm1	APN	5	33,748,800 (GRCm38)	missense	possibly damaging	0.89
IGL01882:Letm1	APN	5	33,769,665 (GRCm38)	missense	probably benign	0.00
IGL02186:Letm1	APN	5	33,745,047 (GRCm38)	missense	probably benign	0.00
IGL02699:Letm1	APN	5	33,745,148 (GRCm38)	missense	possibly damaging	0.93
IGL03089:Letm1	APN	5	33,760,858 (GRCm38)	missense	probably damaging	1.00
R0466:Letm1	UTSW	5	33,761,730 (GRCm38)	splice site	probably benign
R0639:Letm1	UTSW	5	33,769,426 (GRCm38)	missense	possibly damaging	0.88
R1370:Letm1	UTSW	5	33,778,682 (GRCm38)	splice site	probably null
R1415:Letm1	UTSW	5	33,769,562 (GRCm38)	missense	probably benign	0.06
R1511:Letm1	UTSW	5	33,752,555 (GRCm38)	missense	probably damaging	1.00
R1714:Letm1	UTSW	5	33,760,884 (GRCm38)	missense	possibly damaging	0.51
R1771:Letm1	UTSW	5	33,769,467 (GRCm38)	missense	probably damaging	1.00
R1990:Letm1	UTSW	5	33,769,515 (GRCm38)	frame shift	probably null
R1991:Letm1	UTSW	5	33,769,515 (GRCm38)	frame shift	probably null
R2143:Letm1	UTSW	5	33,769,515 (GRCm38)	frame shift	probably null
R2145:Letm1	UTSW	5	33,769,515 (GRCm38)	frame shift	probably null
R2202:Letm1	UTSW	5	33,769,486 (GRCm38)	missense	possibly damaging	0.64
R2290:Letm1	UTSW	5	33,769,515 (GRCm38)	frame shift	probably null
R2292:Letm1	UTSW	5	33,769,515 (GRCm38)	frame shift	probably null
R5574:Letm1	UTSW	5	33,769,386 (GRCm38)	missense	possibly damaging	0.46
R6954:Letm1	UTSW	5	33,782,507 (GRCm38)	missense	probably benign	0.35
R7265:Letm1	UTSW	5	33,778,648 (GRCm38)	missense	possibly damaging	0.62
R8713:Letm1	UTSW	5	33,762,505 (GRCm38)	missense	probably damaging	1.00
R9028:Letm1	UTSW	5	33,752,503 (GRCm38)	missense	probably damaging	1.00
R9420:Letm1	UTSW	5	33,769,458 (GRCm38)	missense	probably damaging	1.00
S24628:Letm1	UTSW	5	33,747,446 (GRCm38)	missense	probably benign
S24628:Letm1	UTSW	5	33,747,444 (GRCm38)	missense	probably benign	0.00
X0066:Letm1	UTSW	5	33,762,571 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CCTACAATAGGGGAGGCTTCTG -3'
(R):5'- GTATAATGGTGCAGCCCAGG -3'

Sequencing Primer
(F):5'- GGCCCACCTCACCTTATCATCAG -3'
(R):5'- TGAGGCTGACAGCTCCTG -3'

Posted On

2021-11-19