Incidental Mutation 'R1370:Letm1'
ID 155933
Institutional Source Beutler Lab
Gene Symbol Letm1
Ensembl Gene ENSMUSG00000005299
Gene Name leucine zipper-EF-hand containing transmembrane protein 1
Synonyms
MMRRC Submission 039434-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.961) question?
Stock # R1370 (G1)
Quality Score 219
Status Validated
Chromosome 5
Chromosomal Location 33897017-33940061 bp(-) (GRCm39)
Type of Mutation splice site
DNA Base Change (assembly) A to T at 33936026 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000143805 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005431] [ENSMUST00000148451]
AlphaFold Q9Z2I0
Predicted Effect probably null
Transcript: ENSMUST00000005431
SMART Domains Protein: ENSMUSP00000005431
Gene: ENSMUSG00000005299

DomainStartEndE-ValueType
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 null
Transcript: ENSMUST00000148451
Predicted Effect probably benign
Transcript: ENSMUST00000200827
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201981
Predicted Effect noncoding transcript
Transcript: ENSMUST00000202183
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 98.7%
  • 3x: 97.5%
  • 10x: 93.6%
  • 20x: 84.8%
Validation Efficiency 99% (80/81)
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
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb10 C T 8: 124,688,791 (GRCm39) G495D probably damaging Het
Adgra3 T C 5: 50,118,129 (GRCm39) I1140V possibly damaging Het
Adrb3 A T 8: 27,717,798 (GRCm39) probably null Het
Afap1 A G 5: 36,092,944 (GRCm39) D16G unknown Het
AI593442 T C 9: 52,589,308 (GRCm39) K90E probably damaging Het
Aicda A T 6: 122,538,144 (GRCm39) N101Y probably benign Het
Alx1 A G 10: 102,864,353 (GRCm39) S39P possibly damaging Het
Ankrd52 A G 10: 128,224,565 (GRCm39) D781G possibly damaging Het
Arhgef5 T A 6: 43,260,846 (GRCm39) F1424I probably damaging Het
Atp10b G A 11: 43,042,482 (GRCm39) W14* probably null Het
Bin1 A G 18: 32,562,756 (GRCm39) I416V probably benign Het
Bptf A T 11: 106,937,920 (GRCm39) S2724T probably damaging Het
Brf1 A T 12: 112,924,728 (GRCm39) probably null Het
Ccdc39 T C 3: 33,880,629 (GRCm39) K446R probably damaging Het
Cd226 T A 18: 89,265,147 (GRCm39) S29T probably benign Het
Cdan1 A G 2: 120,549,620 (GRCm39) probably null Het
Chaf1a A T 17: 56,371,032 (GRCm39) H639L probably benign Het
Chd1 G A 17: 17,607,742 (GRCm39) G430D probably benign Het
Ciao3 A G 17: 25,995,962 (GRCm39) E62G probably benign Het
Clca3a2 T C 3: 144,519,624 (GRCm39) probably benign Het
Clptm1 A G 7: 19,367,797 (GRCm39) V605A possibly damaging Het
Cmpk2 A G 12: 26,521,451 (GRCm39) D241G probably damaging Het
Cryzl1 A G 16: 91,489,546 (GRCm39) V266A possibly damaging Het
Cyp2c68 A G 19: 39,729,400 (GRCm39) L29P probably damaging Het
Dennd3 A C 15: 73,412,703 (GRCm39) probably benign Het
Dennd4c T A 4: 86,729,747 (GRCm39) I783N probably damaging Het
Dock10 A G 1: 80,518,060 (GRCm39) S1305P probably damaging Het
Eml6 T G 11: 29,783,085 (GRCm39) S599R probably benign Het
Gbp8 C T 5: 105,164,442 (GRCm39) A394T possibly damaging Het
H1f10 A G 6: 87,958,133 (GRCm39) I69T probably damaging Het
Herc2 T A 7: 55,818,621 (GRCm39) C2771S probably benign Het
Ism1 A T 2: 139,573,994 (GRCm39) I115F possibly damaging Het
Itga10 C T 3: 96,559,054 (GRCm39) probably benign Het
Itgb8 C T 12: 119,134,738 (GRCm39) G443E probably benign Het
Kalrn T A 16: 33,795,954 (GRCm39) I1274F possibly damaging Het
Klk1b11 A G 7: 43,426,331 (GRCm39) I22V probably benign Het
Krt6b T C 15: 101,585,987 (GRCm39) D362G probably damaging Het
Lce1e A G 3: 92,615,150 (GRCm39) S66P unknown Het
Lrrcc1 G T 3: 14,613,174 (GRCm39) V299L probably benign Het
Mettl5 A T 2: 69,711,764 (GRCm39) probably null Het
Mrpl12 A G 11: 120,376,127 (GRCm39) S46G probably benign Het
Ndrg3 T C 2: 156,780,570 (GRCm39) E198G probably damaging Het
Or5ac16 A G 16: 59,022,043 (GRCm39) S249P probably damaging Het
Pcdh20 A G 14: 88,705,737 (GRCm39) I521T probably benign Het
Pdzph1 T C 17: 59,281,082 (GRCm39) D400G possibly damaging Het
Per2 A T 1: 91,373,279 (GRCm39) S170T possibly damaging Het
Pramel25 T A 4: 143,521,874 (GRCm39) L497I possibly damaging Het
Pros1 A G 16: 62,739,921 (GRCm39) K457E probably benign Het
Rer1 T A 4: 155,160,081 (GRCm39) M156L probably benign Het
Rerg A T 6: 137,034,799 (GRCm39) probably benign Het
Sel1l3 G T 5: 53,357,559 (GRCm39) H144Q possibly damaging Het
Septin2 G T 1: 93,426,828 (GRCm39) V146L probably damaging Het
Setd1b C T 5: 123,298,748 (GRCm39) probably benign Het
Sh3bp4 A T 1: 89,071,494 (GRCm39) Y114F probably benign Het
Slc44a5 C A 3: 153,948,796 (GRCm39) T188K probably benign Het
Slco6d1 A C 1: 98,350,819 (GRCm39) I100L probably benign Het
Slfn4 G T 11: 83,079,632 (GRCm39) D441Y probably damaging Het
Smg1 T C 7: 117,758,975 (GRCm39) probably benign Het
Snrpb2 A G 2: 142,907,086 (GRCm39) probably benign Het
Sspo T A 6: 48,425,560 (GRCm39) S60R probably benign Het
Stard9 T C 2: 120,527,958 (GRCm39) V1405A probably benign Het
Syt1 A G 10: 108,526,783 (GRCm39) L42P probably damaging Het
Tarbp1 T C 8: 127,175,069 (GRCm39) D789G probably benign Het
Tbcel A T 9: 42,361,358 (GRCm39) D63E probably damaging Het
Tdrd3 A T 14: 87,695,490 (GRCm39) probably benign Het
Tiam1 A T 16: 89,695,109 (GRCm39) I116N probably benign Het
Tsc22d1 A G 14: 76,675,104 (GRCm39) probably benign Het
Tsga10 G T 1: 37,874,534 (GRCm39) T117K probably damaging Het
Ttc3 A G 16: 94,219,496 (GRCm39) S492G possibly damaging Het
Ttn G T 2: 76,677,495 (GRCm39) probably benign Het
Wasf3 T C 5: 146,407,018 (GRCm39) probably benign Het
Zbtb37 C T 1: 160,859,592 (GRCm39) E238K probably benign Het
Zfp354c A G 11: 50,706,667 (GRCm39) I136T probably benign Het
Zfp384 G A 6: 125,013,416 (GRCm39) A479T probably benign Het
Zfp646 T A 7: 127,479,036 (GRCm39) N404K probably damaging Het
Other mutations in Letm1
AlleleSourceChrCoordTypePredicted EffectPPH 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
R1415:Letm1 UTSW 5 33,926,906 (GRCm39) missense probably benign 0.06
R1511:Letm1 UTSW 5 33,909,899 (GRCm39) missense probably damaging 1.00
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'- AGGAGGAAGAAGCTGTCAGTTCCC -3'
(R):5'- TGCCAGCAACTGTAGCTGGAAAG -3'

Sequencing Primer
(F):5'- TTCCCTGACAAAGTCCAGGTG -3'
(R):5'- GAGAGCCCACCTTCCTCAG -3'
Posted On 2014-02-11