Mutagenetix > Incidental Mutation

Incidental Mutation 'R9028:Letm1'

686862

Institutional Source

Beutler Lab

Gene Symbol

Letm1

Ensembl Gene

ENSMUSG00000005299

Gene Name

leucine zipper-EF-hand containing transmembrane protein 1

Synonyms

MMRRC Submission

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.961) question?

Stock #

R9028 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

33739673-33782817 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 33752503 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Lysine at position 396 (Q396K)

Ref Sequence

ENSEMBL: ENSMUSP00000005431 (fasta)

Gene Model

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

AlphaFold

Q9Z2I0

Predicted Effect

probably damaging
Transcript: ENSMUST00000005431
AA Change: Q396K

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000005431
Gene: ENSMUSG00000005299
AA Change: Q396K

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.2%

Validation Efficiency

99% (74/75)

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: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5330417C22Rik	G	A	3: 108,463,503	T687I	probably benign	Het
Aasdh	A	G	5: 76,876,130	V1066A	probably damaging	Het
Abca5	T	A	11: 110,298,078	H851L	probably damaging	Het
Actn2	T	C	13: 12,300,978	I218M	possibly damaging	Het
Afmid	G	A	11: 117,836,663	E338K	probably benign	Het
Amer3	G	A	1: 34,588,677	V666I	probably benign	Het
Apol7b	A	G	15: 77,423,416	V293A	probably damaging	Het
Bag6	T	A	17: 35,144,154	S657T	probably benign	Het
Btaf1	T	C	19: 36,969,108	L438P	probably damaging	Het
Cdc20	T	C	4: 118,436,560	E126G	probably benign	Het
Cep97	C	T	16: 55,919,552	W248*	probably null	Het
Cfap69	A	T	5: 5,646,958	S113T	probably benign	Het
Cgrrf1	C	A	14: 46,853,743	D241E	probably benign	Het
Cnksr1	T	C	4: 134,233,297	T280A	possibly damaging	Het
Cox4i1	T	A	8: 120,671,283		probably benign	Het
Cpm	T	A	10: 117,683,509	F441I	probably benign	Het
Cs	A	C	10: 128,353,083	M154L		Het
Dmrta1	T	A	4: 89,691,677	N291K	probably damaging	Het
Dnah7a	T	C	1: 53,521,138	T2125A	probably benign	Het
Dock10	A	T	1: 80,606,295		probably benign	Het
Dok7	A	G	5: 35,079,475	Y369C	probably damaging	Het
E130311K13Rik	T	C	3: 63,915,548	Y225C	probably damaging	Het
F7	T	C	8: 13,026,087	L10P	possibly damaging	Het
Faf1	C	A	4: 109,890,908	T470K	possibly damaging	Het
Fam83h	A	T	15: 76,003,889	L533Q	possibly damaging	Het
Far1	T	A	7: 113,547,422	V129E	probably damaging	Het
Fgfr4	T	C	13: 55,159,154	Y219H	probably damaging	Het
Fryl	A	T	5: 73,098,266	S807R	probably benign	Het
Gaa	T	A	11: 119,270,381	D83E	probably benign	Het
Gm6970	T	C	19: 47,170,690	K149E	unknown	Het
Grm2	A	G	9: 106,651,185	S167P	possibly damaging	Het
Hibch	T	C	1: 52,853,709	L26P	possibly damaging	Het
Hspa9	T	C	18: 34,942,031	E415G	probably damaging	Het
Ipo4	T	C	14: 55,628,951	Y757C	probably damaging	Het
Itk	T	A	11: 46,344,883		probably benign	Het
Kdm5a	C	T	6: 120,439,131	P1671S	probably benign	Het
Kif13a	G	A	13: 46,798,365	P811S	probably damaging	Het
Kif23	T	C	9: 61,921,059	E857G	probably damaging	Het
Kif2b	A	G	11: 91,577,185	S91P	probably benign	Het
Map2k6	T	A	11: 110,497,973	M247K		Het
Mga	A	G	2: 119,947,589	I1872V	probably benign	Het
Mmp15	A	T	8: 95,369,688	N369I	probably benign	Het
Myo3a	T	A	2: 22,600,087	S1487T	possibly damaging	Het
Ncam1	T	C	9: 49,507,436	T855A		Het
Ncoa2	A	G	1: 13,152,855	V1182A	probably benign	Het
Nhlrc3	A	T	3: 53,453,571	C254*	probably null	Het
Nlrp1a	C	T	11: 71,122,993	R477H	probably benign	Het
Nox3	T	A	17: 3,665,910	T407S	possibly damaging	Het
Olfr1229	T	A	2: 89,282,332	D267V	probably damaging	Het
Olfr1375	C	T	11: 51,048,833	T242M	probably damaging	Het
Olfr411	T	C	11: 74,346,921	Y101C	probably damaging	Het
Pfkp	T	A	13: 6,605,689	I303F	probably damaging	Het
Pgc	T	C	17: 47,733,058	Y292H	possibly damaging	Het
Phtf2	A	G	5: 20,794,375	Y257H	probably benign	Het
Pkdrej	T	C	15: 85,816,897	N1613D	probably damaging	Het
Prpmp5	C	T	6: 132,312,655	E69K	unknown	Het
Rapgef2	A	G	3: 79,074,344	S1115P	probably damaging	Het
Rbpj	A	G	5: 53,649,690	E260G	possibly damaging	Het
Rrm1	T	A	7: 102,460,398	N476K	probably damaging	Het
Slc9a2	T	A	1: 40,726,452	I334N	probably damaging	Het
Slk	T	G	19: 47,620,073	N488K	probably benign	Het
Smarca5	T	C	8: 80,714,013	I607M	probably damaging	Het
Sspo	G	A	6: 48,496,153	V162M	probably benign	Het
Svep1	T	G	4: 58,145,199	Q422P	possibly damaging	Het
Tcn2	C	T	11: 3,922,111	V339I	probably damaging	Het
Tnfrsf19	T	C	14: 61,005,201	H78R	probably benign	Het
Trav14-3	C	A	14: 53,763,430	Q33K	unknown	Het
Ubtd2	T	C	11: 32,499,432	I93T	possibly damaging	Het
Uhrf2	G	A	19: 30,089,344		probably null	Het
Vmn1r224	T	G	17: 20,419,850	S230A	possibly damaging	Het
Wee2	A	T	6: 40,444,255	H93L	probably benign	Het
Zdhhc17	T	C	10: 110,961,073	E279G	probably damaging	Het
Zfp623	T	A	15: 75,947,500	F102I	probably damaging	Het
Zfpm2	A	C	15: 41,103,362	E1081A	possibly damaging	Het
Zscan18	A	T	7: 12,772,189		probably benign	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
R1771:Letm1	UTSW	5	33769467	missense	probably damaging	1.00
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
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'- GCCAGATATGCATTTACTTGGG -3'
(R):5'- CCCAGTTGTGTTAACATCAGTGTC -3'

Sequencing Primer
(F):5'- GAGGCTTTTCTAGTTTGAAGACCACC -3'
(R):5'- ACATCAGTGTCATAGATCTGGAATG -3'

Posted On

2021-11-19