Incidental Mutation 'IGL03089:Letm1'
ID 418285
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Letm1
Ensembl Gene ENSMUSG00000005299
Gene Name leucine zipper-EF-hand containing transmembrane protein 1
Accession Numbers
Essential gene? Probably essential (E-score: 0.957) question?
Stock # IGL03089
Quality Score
Chromosome 5
Chromosomal Location 33739673-33782817 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to A at 33760858 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Aspartic acid at position 314 (E314D)
Ref Sequence ENSEMBL: ENSMUSP00000005431 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005431]
AlphaFold Q9Z2I0
Predicted Effect probably damaging
Transcript: ENSMUST00000005431
AA Change: E314D

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000005431
Gene: ENSMUSG00000005299
AA Change: E314D

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: ENSMUST00000131139
Predicted Effect probably benign
Transcript: ENSMUST00000200827
Coding Region Coverage
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: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamtsl4 A G 3: 95,677,246 (GRCm38) S947P probably damaging Het
Agl T A 3: 116,781,023 (GRCm38) H709L probably damaging Het
Alpi T A 1: 87,100,108 (GRCm38) D250V probably benign Het
Anapc4 A G 5: 52,866,398 (GRCm38) S735G probably benign Het
Ank1 A T 8: 23,104,832 (GRCm38) I611L probably benign Het
Canx A G 11: 50,304,482 (GRCm38) V253A possibly damaging Het
Cbfa2t3 A T 8: 122,635,134 (GRCm38) I383N probably damaging Het
Cdc23 T C 18: 34,634,460 (GRCm38) Y519C probably damaging Het
Celsr3 T A 9: 108,826,607 (GRCm38) N96K probably benign Het
Clptm1 A G 7: 19,637,147 (GRCm38) Y355H probably damaging Het
Col6a5 C T 9: 105,933,839 (GRCm38) S827N unknown Het
Cyp21a1 G T 17: 34,803,446 (GRCm38) probably null Het
Cyp24a1 T G 2: 170,485,966 (GRCm38) H452P probably damaging Het
Cyp2c39 T A 19: 39,563,851 (GRCm38) H329Q probably benign Het
D630003M21Rik C T 2: 158,216,744 (GRCm38) R412Q probably benign Het
Dennd1b G A 1: 139,102,029 (GRCm38) R308Q possibly damaging Het
Deup1 T C 9: 15,607,800 (GRCm38) S137G possibly damaging Het
Dmbt1 T A 7: 131,111,049 (GRCm38) I1583N probably damaging Het
Dvl1 G A 4: 155,855,152 (GRCm38) V320M probably damaging Het
Elmod3 A G 6: 72,569,316 (GRCm38) S254P probably damaging Het
Emsy G A 7: 98,637,266 (GRCm38) Q226* probably null Het
Ephb6 C A 6: 41,614,174 (GRCm38) D88E probably damaging Het
Exoc1 A G 5: 76,542,158 (GRCm38) M182V possibly damaging Het
Fbxw4 T G 19: 45,591,721 (GRCm38) probably benign Het
Fgr A G 4: 132,986,266 (GRCm38) D35G probably damaging Het
Gm13078 A G 4: 143,726,133 (GRCm38) T45A probably benign Het
Gm20547 A T 17: 34,861,032 (GRCm38) D366E probably damaging Het
Gucy1a1 T C 3: 82,097,681 (GRCm38) N599S probably damaging Het
Ighg2b G A 12: 113,306,678 (GRCm38) P240L probably damaging Het
Jak3 A G 8: 71,686,083 (GRCm38) D975G probably benign Het
Klhl26 A T 8: 70,455,633 (GRCm38) N24K probably benign Het
Lin54 A T 5: 100,450,993 (GRCm38) F319L probably damaging Het
Lrp5 A T 19: 3,620,314 (GRCm38) probably null Het
Lvrn T C 18: 46,880,709 (GRCm38) F486S probably damaging Het
Nov C T 15: 54,749,284 (GRCm38) R230C possibly damaging Het
Olfr1218 T C 2: 89,055,013 (GRCm38) R138G probably benign Het
Olfr378 T C 11: 73,425,183 (GRCm38) T267A probably benign Het
Olfr631 A C 7: 103,929,122 (GRCm38) I100L probably benign Het
Olfr93 A G 17: 37,151,643 (GRCm38) C110R probably damaging Het
Olfr969 A T 9: 39,795,681 (GRCm38) Y102F probably benign Het
Sap30bp T A 11: 115,957,388 (GRCm38) M112K possibly damaging Het
Sbno1 A G 5: 124,387,311 (GRCm38) probably benign Het
Slc30a5 T C 13: 100,813,830 (GRCm38) I307V probably benign Het
Trim37 T A 11: 87,190,137 (GRCm38) D21E probably damaging Het
Usp34 T C 11: 23,446,958 (GRCm38) F614S possibly damaging Het
Usp39 A C 6: 72,328,639 (GRCm38) F387C probably damaging Het
Vipas39 C T 12: 87,253,254 (GRCm38) C149Y probably damaging Het
Vmn2r107 C A 17: 20,375,712 (GRCm38) H842Q probably benign Het
Vps18 T A 2: 119,293,177 (GRCm38) V195E probably benign Het
Vsx1 A G 2: 150,685,590 (GRCm38) probably benign Het
Other mutations in Letm1
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
R9061:Letm1 UTSW 5 33,760,869 (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
Posted On 2016-08-02