Incidental Mutation 'IGL01013:Letm1'
ID 53571
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 # IGL01013
Quality Score
Chromosome 5
Chromosomal Location 33739673-33782817 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to T at 33762590 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Cysteine to Serine at position 202 (C202S)
Ref Sequence ENSEMBL: ENSMUSP00000005431 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005431]
AlphaFold Q9Z2I0
Predicted Effect possibly damaging
Transcript: ENSMUST00000005431
AA Change: C202S

PolyPhen 2 Score 0.817 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000005431
Gene: ENSMUSG00000005299
AA Change: C202S

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: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aasdh T A 5: 76,886,206 (GRCm38) E499D possibly damaging Het
Abca1 A T 4: 53,038,185 (GRCm38) L2059* probably null Het
Ankar T A 1: 72,650,989 (GRCm38) I1228F possibly damaging Het
Appl1 A T 14: 26,949,476 (GRCm38) Y340N possibly damaging Het
Atp8b4 C A 2: 126,323,087 (GRCm38) R1103L probably benign Het
B4galt6 A G 18: 20,689,013 (GRCm38) V308A probably damaging Het
Ccdc162 G A 10: 41,581,339 (GRCm38) P1534L probably benign Het
Ccdc78 A G 17: 25,789,054 (GRCm38) E313G possibly damaging Het
Cep57l1 G A 10: 41,740,869 (GRCm38) R141* probably null Het
Cpsf1 G A 15: 76,599,297 (GRCm38) Q883* probably null Het
Crot A G 5: 8,993,575 (GRCm38) Y16H probably benign Het
Cyld T G 8: 88,742,362 (GRCm38) L587R probably damaging Het
Fam114a1 G A 5: 65,031,395 (GRCm38) probably null Het
Fam89b G T 19: 5,729,369 (GRCm38) D53E probably benign Het
Fig4 T C 10: 41,267,786 (GRCm38) M226V probably benign Het
Gm10722 A T 9: 3,002,230 (GRCm38) Y184F probably damaging Het
Hp C A 8: 109,579,021 (GRCm38) probably benign Het
Igsf9b G T 9: 27,334,304 (GRCm38) R1189L probably damaging Het
Ilf3 A G 9: 21,399,691 (GRCm38) N620D possibly damaging Het
Jakmip3 A C 7: 139,017,573 (GRCm38) E228A possibly damaging Het
Kpna3 A T 14: 61,370,517 (GRCm38) I413K probably damaging Het
Lmod2 C A 6: 24,604,135 (GRCm38) Q370K probably damaging Het
Map4k5 T C 12: 69,827,526 (GRCm38) probably benign Het
Mcidas T A 13: 112,997,585 (GRCm38) probably benign Het
Mme A G 3: 63,327,860 (GRCm38) probably null Het
Mrc1 T C 2: 14,328,425 (GRCm38) W1306R probably damaging Het
Mthfd1l C A 10: 4,030,716 (GRCm38) Q473K probably damaging Het
Muc6 A T 7: 141,648,066 (GRCm38) C719* probably null Het
Nsun7 T C 5: 66,283,601 (GRCm38) I355T possibly damaging Het
Padi6 A G 4: 140,729,003 (GRCm38) L560P probably damaging Het
Parl C A 16: 20,282,790 (GRCm38) A285S possibly damaging Het
Pclo A T 5: 14,793,834 (GRCm38) M4795L unknown Het
Polr2f A G 15: 79,146,129 (GRCm38) Y56C probably damaging Het
Rasgrp2 A T 19: 6,404,383 (GRCm38) H152L probably damaging Het
Rpl10l T C 12: 66,284,227 (GRCm38) D44G probably benign Het
Slc25a16 A G 10: 62,944,433 (GRCm38) probably null Het
Snrnp200 G A 2: 127,232,472 (GRCm38) E1411K probably damaging Het
Tanc2 G A 11: 105,625,065 (GRCm38) R3Q probably damaging Het
Tbc1d32 G T 10: 56,201,959 (GRCm38) probably null Het
Tcf7l2 T C 19: 55,919,627 (GRCm38) probably benign Het
Tnrc6c G T 11: 117,722,029 (GRCm38) V498L probably benign Het
Tymp G A 15: 89,376,310 (GRCm38) H102Y probably damaging Het
Wdr76 T C 2: 121,535,497 (GRCm38) S492P probably benign Het
Zc3h12d T C 10: 7,839,956 (GRCm38) I41T probably damaging Het
Other mutations in Letm1
AlleleSourceChrCoordTypePredicted EffectPPH Score
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
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 2013-06-28