Incidental Mutation 'R7407:Letmd1'
ID574814
Institutional Source Beutler Lab
Gene Symbol Letmd1
Ensembl Gene ENSMUSG00000037353
Gene NameLETM1 domain containing 1
SynonymsHCCR1, 1110019O13Rik, HCCR-2
MMRRC Submission
Accession Numbers

Ncbi RefSeq: NM_134093.2; MGI:1915864

Is this an essential gene? Probably non essential (E-score: 0.135) question?
Stock #R7407 (G1)
Quality Score225.009
Status Not validated
Chromosome15
Chromosomal Location100469023-100479164 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) G to T at 100469238 bp
ZygosityHeterozygous
Amino Acid Change Alanine to Serine at position 39 (A39S)
Ref Sequence ENSEMBL: ENSMUSP00000037546 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000037001] [ENSMUST00000229012] [ENSMUST00000229648] [ENSMUST00000230294]
Predicted Effect probably benign
Transcript: ENSMUST00000037001
AA Change: A39S

PolyPhen 2 Score 0.084 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000037546
Gene: ENSMUSG00000037353
AA Change: A39S

DomainStartEndE-ValueType
Pfam:LETM1 78 346 1.5e-72 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000229012
AA Change: A39S

PolyPhen 2 Score 0.427 (Sensitivity: 0.89; Specificity: 0.90)
Predicted Effect probably benign
Transcript: ENSMUST00000229648
Predicted Effect probably benign
Transcript: ENSMUST00000230294
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a mitochondrial outer membrane protein. It has a potential role in tumorigenesis, which may result from negative regulation of the p53 tumor suppressor gene. Alternatively spliced transcript variants have been noted for this gene. [provided by RefSeq, Aug 2011]
Allele List at MGI

All alleles(7) : Targeted(2) Gene trapped(5)

Other mutations in this stock
Total: 48 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933405O20Rik A G 7: 50,599,878 N220S probably damaging Het
Abcb8 T C 5: 24,400,676 V186A probably benign Het
Actbl2 A T 13: 111,256,218 E362D probably damaging Het
Adamts17 C A 7: 67,047,556 Y28* probably null Het
Agtr1b T C 3: 20,315,731 D237G possibly damaging Het
Amer2 A G 14: 60,378,842 D162G probably damaging Het
Ankub1 T C 3: 57,665,203 E366G probably benign Het
Ap5z1 A G 5: 142,466,575 I88V probably benign Het
BC053393 A G 11: 46,577,390 Y97C probably damaging Het
Ccdc186 T C 19: 56,813,385 N100S probably benign Het
Cldn19 A G 4: 119,255,685 D38G probably damaging Het
Crat C T 2: 30,404,565 R497Q probably benign Het
Deaf1 G A 7: 141,297,579 A545V possibly damaging Het
Dicer1 G T 12: 104,722,351 Y322* probably null Het
Dnajb7 G T 15: 81,407,626 T170K possibly damaging Het
Flrt2 A T 12: 95,779,300 E137D probably damaging Het
Galnt12 T C 4: 47,120,362 F482L probably damaging Het
Gm14025 A G 2: 129,038,809 I399T Het
Gm32742 A G 9: 51,156,674 V336A probably damaging Het
Gpatch8 G A 11: 102,479,830 R961W unknown Het
Hcn4 A G 9: 58,859,370 E738G unknown Het
Kdelr3 A G 15: 79,524,838 Y76C probably damaging Het
Krt77 T C 15: 101,860,095 S494G unknown Het
Lrrc7 G A 3: 158,135,241 R1387W probably damaging Het
Meltf T C 16: 31,894,735 Y599H probably damaging Het
Mybpc1 T A 10: 88,549,347 I477L probably damaging Het
Nf1 A G 11: 79,448,143 D1174G probably damaging Het
Olfr720 T A 14: 14,175,402 I227L probably benign Het
Olfr907 T A 9: 38,499,504 Y278* probably null Het
Palld G T 8: 61,515,941 S1283* probably null Het
Pcmtd2 T C 2: 181,846,605 V183A possibly damaging Het
Pcsk5 T A 19: 17,675,516 I269F probably damaging Het
Pkd1 T C 17: 24,594,594 L4036P probably damaging Het
Pkhd1l1 A G 15: 44,595,011 N4151S possibly damaging Het
Rcor3 C T 1: 192,101,672 S422N probably benign Het
Rhag A G 17: 40,831,334 I223V possibly damaging Het
Ssbp4 A G 8: 70,599,022 Y231H probably damaging Het
Syce1l C T 8: 113,655,138 Q237* probably null Het
Tenm4 T C 7: 96,773,987 V663A possibly damaging Het
Trim6 T C 7: 104,225,901 I115T probably damaging Het
Vmn1r25 T A 6: 57,979,059 T82S possibly damaging Het
Vmn2r28 A G 7: 5,481,309 S631P probably damaging Het
Xpo1 T A 11: 23,285,823 V637E probably damaging Het
Xpo6 A T 7: 126,171,052 M62K probably damaging Het
Ypel5 A G 17: 72,846,379 N26S possibly damaging Het
Zbtb24 C A 10: 41,464,779 Q624K possibly damaging Het
Zfp629 T C 7: 127,610,243 D798G probably benign Het
Zfp687 C T 3: 95,007,530 R1220H probably damaging Het
Other mutations in Letmd1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01020:Letmd1 APN 15 100471759 missense probably damaging 1.00
IGL02210:Letmd1 APN 15 100469247 critical splice donor site probably null
IGL02486:Letmd1 APN 15 100475111 missense probably damaging 1.00
IGL02606:Letmd1 APN 15 100475091 missense probably damaging 1.00
IGL03218:Letmd1 APN 15 100469828 missense probably damaging 1.00
P0031:Letmd1 UTSW 15 100472609 missense probably damaging 1.00
PIT4515001:Letmd1 UTSW 15 100476802 missense probably damaging 1.00
R0737:Letmd1 UTSW 15 100469821 missense probably damaging 1.00
R1466:Letmd1 UTSW 15 100472542 splice site probably null
R1466:Letmd1 UTSW 15 100472542 splice site probably null
R1584:Letmd1 UTSW 15 100472542 splice site probably null
R4457:Letmd1 UTSW 15 100475130 missense possibly damaging 0.54
R4641:Letmd1 UTSW 15 100477827 missense probably damaging 1.00
R4724:Letmd1 UTSW 15 100469738 missense probably damaging 1.00
R5463:Letmd1 UTSW 15 100469128 missense probably damaging 1.00
Y5407:Letmd1 UTSW 15 100475409 critical splice donor site probably null
Predicted Primers PCR Primer
(F):5'- ACTGGGTTCCTCAAGGAGAC -3'
(R):5'- TGCAAGCTGAAGCCATGGAG -3'

Sequencing Primer
(F):5'- TCACGATAGCGACCTCAGG -3'
(R):5'- ATGAGCTCAGGATGTGCG -3'
Posted On2019-10-07