Incidental Mutation 'R7976:Lyrm1'
ID 650909
Institutional Source Beutler Lab
Gene Symbol Lyrm1
Ensembl Gene ENSMUSG00000030922
Gene Name LYR motif containing 1
Synonyms 2310004B22Rik, 1110065L10Rik, 4930404J24Rik
MMRRC Submission 046019-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.330) question?
Stock # R7976 (G1)
Quality Score 225.009
Status Not validated
Chromosome 7
Chromosomal Location 119495038-119515979 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 119515449 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 113 (V113A)
Ref Sequence ENSEMBL: ENSMUSP00000146648 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000054440] [ENSMUST00000106516] [ENSMUST00000106517] [ENSMUST00000106518] [ENSMUST00000207270] [ENSMUST00000208202] [ENSMUST00000208424]
AlphaFold Q9CQB7
Predicted Effect probably benign
Transcript: ENSMUST00000054440
AA Change: V113A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000051616
Gene: ENSMUSG00000030922
AA Change: V113A

DomainStartEndE-ValueType
Pfam:Complex1_LYR 7 73 4.5e-19 PFAM
Pfam:Complex1_LYR_1 7 74 2.4e-14 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000106516
AA Change: V113A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000102126
Gene: ENSMUSG00000030922
AA Change: V113A

DomainStartEndE-ValueType
Pfam:Complex1_LYR 7 73 4.5e-19 PFAM
Pfam:Complex1_LYR_1 7 74 2.4e-14 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000106517
AA Change: V113A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000102127
Gene: ENSMUSG00000030922
AA Change: V113A

DomainStartEndE-ValueType
Pfam:Complex1_LYR 7 73 4.5e-19 PFAM
Pfam:Complex1_LYR_1 7 74 2.4e-14 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000106518
AA Change: V113A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000102128
Gene: ENSMUSG00000030922
AA Change: V113A

DomainStartEndE-ValueType
Pfam:Complex1_LYR 7 73 4.5e-19 PFAM
Pfam:Complex1_LYR_1 7 74 2.4e-14 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000207270
AA Change: V113A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
Predicted Effect probably benign
Transcript: ENSMUST00000208202
AA Change: V113A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
Predicted Effect probably benign
Transcript: ENSMUST00000208424
AA Change: V113A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.2%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene belongs to the mitochondrial leucine/tyrosine/arginine motif family of proteins. Proteins of this family are short polypeptides that contain a leucine/tyrosine/arginine motif near the N-terminus. This gene is widely expressed with high levels in omental adipose tissue of obese individuals. In adipose tissue, the protein is localized to the nucleus where it promotes preadipocyte proliferation and lowers the rate of apoptosis to regulate adipose tissue homeostasis. Overexpression of this gene in adipocytes causes abnormal mitochondrial morphology and mitochondrial dysfunction. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]
Allele List at MGI
Other mutations in this stock
Total: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adss1 A C 12: 112,602,831 (GRCm39) I341L probably benign Het
Aldh1b1 T A 4: 45,803,092 (GRCm39) M210K possibly damaging Het
Ankrd17 G A 5: 90,431,451 (GRCm39) Q778* probably null Het
Bmper T C 9: 23,318,106 (GRCm39) V575A probably damaging Het
Brinp2 A G 1: 158,073,913 (GRCm39) V736A probably benign Het
Ccdc81 A T 7: 89,515,723 (GRCm39) L652* probably null Het
Cdt1 C T 8: 123,298,585 (GRCm39) R437W probably damaging Het
Ckb A C 12: 111,637,466 (GRCm39) L165R possibly damaging Het
Col25a1 G T 3: 130,290,075 (GRCm39) G255V probably damaging Het
Ddx17 A G 15: 79,420,156 (GRCm39) probably null Het
Dennd4a G T 9: 64,759,794 (GRCm39) G300W possibly damaging Het
Dlg4 T A 11: 69,930,008 (GRCm39) I316N probably damaging Het
Dlgap2 C T 8: 14,793,410 (GRCm39) P467L probably benign Het
Dnah9 T C 11: 65,732,227 (GRCm39) I4226M possibly damaging Het
Drc1 G A 5: 30,521,829 (GRCm39) A734T probably benign Het
Entpd1 A G 19: 40,600,865 (GRCm39) M1V probably null Het
Exph5 T G 9: 53,287,935 (GRCm39) I1672S possibly damaging Het
Fam149b T A 14: 20,427,852 (GRCm39) D379E probably damaging Het
Fgfr2 T C 7: 129,787,074 (GRCm39) T461A probably damaging Het
Frem1 A G 4: 82,919,946 (GRCm39) V469A probably damaging Het
Frem3 A T 8: 81,338,231 (GRCm39) K175* probably null Het
Fsd2 C T 7: 81,209,629 (GRCm39) G71E probably benign Het
Gcat T C 15: 78,919,188 (GRCm39) I116T probably damaging Het
Gigyf2 G A 1: 87,331,458 (GRCm39) S202N unknown Het
Glra3 T G 8: 56,565,911 (GRCm39) probably null Het
Golga4 C T 9: 118,365,836 (GRCm39) T296I possibly damaging Het
Herc1 C T 9: 66,341,552 (GRCm39) T1816I possibly damaging Het
Igfbpl1 C A 4: 45,826,786 (GRCm39) R3L unknown Het
Ighv15-2 A T 12: 114,528,470 (GRCm39) S28T probably benign Het
Kat2b T A 17: 53,955,835 (GRCm39) M427K probably benign Het
Kdm4c A G 4: 74,295,906 (GRCm39) T882A probably damaging Het
Kif1a G T 1: 92,967,496 (GRCm39) F1138L probably damaging Het
Klhl20 A T 1: 160,934,307 (GRCm39) S237R probably benign Het
Lamc1 A T 1: 153,123,014 (GRCm39) N725K probably damaging Het
Lmtk3 A G 7: 45,444,890 (GRCm39) D1191G unknown Het
Ltbp1 C A 17: 75,670,358 (GRCm39) N1466K possibly damaging Het
Ly75 T C 2: 60,195,432 (GRCm39) E242G probably damaging Het
Mfsd13a G T 19: 46,360,446 (GRCm39) A333S probably benign Het
Mllt10 T C 2: 18,167,214 (GRCm39) S380P possibly damaging Het
Mrc2 A G 11: 105,238,829 (GRCm39) K1295E possibly damaging Het
Muc5ac A T 7: 141,363,528 (GRCm39) I2280F unknown Het
Neurod2 A C 11: 98,218,023 (GRCm39) F380L probably damaging Het
Ntrk3 G A 7: 78,005,954 (GRCm39) A469V probably damaging Het
Nup205 T C 6: 35,175,888 (GRCm39) F584L probably damaging Het
Oas1d A T 5: 121,057,210 (GRCm39) Y272F probably damaging Het
Olfm3 T C 3: 114,874,794 (GRCm39) V30A probably benign Het
Or4c110 T A 2: 88,831,973 (GRCm39) I220F probably damaging Het
Or5b117 A G 19: 13,431,563 (GRCm39) I106T probably benign Het
Or8k22 A G 2: 86,163,064 (GRCm39) V212A probably benign Het
Pcdhga12 A G 18: 37,901,427 (GRCm39) Y753C probably damaging Het
Phox2b A G 5: 67,253,514 (GRCm39) V294A unknown Het
Prdm2 A T 4: 142,859,812 (GRCm39) C1159* probably null Het
Ptpn12 G T 5: 21,207,631 (GRCm39) S275* probably null Het
Rigi T C 4: 40,209,894 (GRCm39) M725V probably damaging Het
Rnf223 A T 4: 156,216,776 (GRCm39) E50D probably damaging Het
Rrp12 A T 19: 41,879,548 (GRCm39) Y169N probably benign Het
Sgip1 T C 4: 102,757,736 (GRCm39) probably null Het
Shank2 T C 7: 143,964,798 (GRCm39) I802T probably damaging Het
Skint2 A T 4: 112,481,329 (GRCm39) N64I probably damaging Het
Smpd3 A C 8: 106,982,254 (GRCm39) C617G probably benign Het
Tmem106c G C 15: 97,865,985 (GRCm39) G192R probably damaging Het
Tmem72 T C 6: 116,673,800 (GRCm39) H106R probably damaging Het
Upf2 G C 2: 6,030,926 (GRCm39) V789L unknown Het
Vash1 A G 12: 86,726,758 (GRCm39) probably benign Het
Vmn1r201 T A 13: 22,658,875 (GRCm39) Y30N probably benign Het
Xpr1 A G 1: 155,166,035 (GRCm39) F571L possibly damaging Het
Yif1a T C 19: 5,139,815 (GRCm39) S87P probably damaging Het
Zer1 T C 2: 29,997,520 (GRCm39) Y462C probably damaging Het
Zfp597 G A 16: 3,684,375 (GRCm39) P127L possibly damaging Het
Zxdc T C 6: 90,375,749 (GRCm39) S742P probably benign Het
Other mutations in Lyrm1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL03062:Lyrm1 APN 7 119,515,354 (GRCm39) splice site probably benign
IGL03130:Lyrm1 APN 7 119,513,403 (GRCm39) missense probably damaging 1.00
IGL03338:Lyrm1 APN 7 119,513,469 (GRCm39) missense probably benign 0.18
R5394:Lyrm1 UTSW 7 119,513,471 (GRCm39) missense possibly damaging 0.93
R9505:Lyrm1 UTSW 7 119,509,090 (GRCm39) missense possibly damaging 0.47
Predicted Primers PCR Primer
(F):5'- GAGTCTGTGGTCGATTTAGCAC -3'
(R):5'- AATGTCATAGTTCAAGCAGCAAGC -3'

Sequencing Primer
(F):5'- CTGTGGTCGATTTAGCACTGAAAAAC -3'
(R):5'- AAACCTTAGGGATGCCTGC -3'
Posted On 2020-09-15