Incidental Mutation 'R5931:Lrrtm4'
ID 461840
Institutional Source Beutler Lab
Gene Symbol Lrrtm4
Ensembl Gene ENSMUSG00000052581
Gene Name leucine rich repeat transmembrane neuronal 4
Synonyms 7530419J18Rik
MMRRC Submission 044126-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.100) question?
Stock # R5931 (G1)
Quality Score 225
Status Not validated
Chromosome 6
Chromosomal Location 79995860-80787124 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 79998722 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 44 (I44V)
Ref Sequence ENSEMBL: ENSMUSP00000114425 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000074662] [ENSMUST00000126005] [ENSMUST00000126399] [ENSMUST00000128718] [ENSMUST00000133918] [ENSMUST00000136421] [ENSMUST00000145407] [ENSMUST00000147663]
AlphaFold Q80XG9
Predicted Effect possibly damaging
Transcript: ENSMUST00000074662
AA Change: I44V

PolyPhen 2 Score 0.700 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000074232
Gene: ENSMUSG00000052581
AA Change: I44V

DomainStartEndE-ValueType
signal peptide 1 30 N/A INTRINSIC
LRRNT 33 65 1.66e0 SMART
LRR_TYP 84 107 6.67e-2 SMART
LRR 108 131 3.52e-1 SMART
LRR_TYP 132 155 2.53e-2 SMART
LRR 156 179 1.16e-1 SMART
LRR 180 203 4.34e-1 SMART
LRR 204 224 2.4e1 SMART
LRR 228 251 4.97e0 SMART
LRR 252 275 1.07e0 SMART
LRR 276 299 1.64e-1 SMART
Blast:LRRCT 311 361 4e-25 BLAST
low complexity region 375 392 N/A INTRINSIC
transmembrane domain 425 447 N/A INTRINSIC
low complexity region 464 469 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000126005
AA Change: I44V

PolyPhen 2 Score 0.700 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000117445
Gene: ENSMUSG00000052581
AA Change: I44V

DomainStartEndE-ValueType
signal peptide 1 30 N/A INTRINSIC
LRRNT 33 65 1.66e0 SMART
LRR_TYP 84 107 6.67e-2 SMART
LRR 108 131 3.52e-1 SMART
LRR_TYP 132 155 2.53e-2 SMART
LRR 156 179 1.16e-1 SMART
LRR 180 203 4.34e-1 SMART
LRR 204 224 2.4e1 SMART
LRR 228 251 4.97e0 SMART
LRR 252 275 1.07e0 SMART
LRR 276 299 1.64e-1 SMART
Blast:LRRCT 311 361 4e-25 BLAST
low complexity region 375 392 N/A INTRINSIC
transmembrane domain 425 447 N/A INTRINSIC
low complexity region 464 469 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000126399
AA Change: I44V

PolyPhen 2 Score 0.700 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000121124
Gene: ENSMUSG00000052581
AA Change: I44V

DomainStartEndE-ValueType
signal peptide 1 30 N/A INTRINSIC
LRRNT 33 65 1.66e0 SMART
LRR_TYP 84 107 6.67e-2 SMART
LRR 108 131 3.52e-1 SMART
LRR_TYP 132 155 2.53e-2 SMART
LRR 156 179 1.16e-1 SMART
LRR 180 203 4.34e-1 SMART
LRR 204 224 2.4e1 SMART
LRR 228 251 4.97e0 SMART
LRR 252 275 1.07e0 SMART
LRR 276 299 1.64e-1 SMART
Blast:LRRCT 311 361 2e-25 BLAST
low complexity region 375 392 N/A INTRINSIC
transmembrane domain 425 447 N/A INTRINSIC
low complexity region 464 469 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000128718
AA Change: I44V

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130734
Predicted Effect possibly damaging
Transcript: ENSMUST00000133918
AA Change: I44V

PolyPhen 2 Score 0.700 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000115016
Gene: ENSMUSG00000052581
AA Change: I44V

DomainStartEndE-ValueType
signal peptide 1 30 N/A INTRINSIC
LRRNT 33 65 1.66e0 SMART
LRR_TYP 84 107 6.67e-2 SMART
LRR 108 131 3.52e-1 SMART
LRR_TYP 132 155 2.53e-2 SMART
LRR 156 179 1.16e-1 SMART
LRR 180 203 4.34e-1 SMART
LRR 204 224 2.4e1 SMART
LRR 228 251 4.97e0 SMART
LRR 252 275 1.07e0 SMART
LRR 276 299 1.64e-1 SMART
Blast:LRRCT 311 361 2e-25 BLAST
low complexity region 375 392 N/A INTRINSIC
transmembrane domain 425 447 N/A INTRINSIC
low complexity region 464 469 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000136421
AA Change: I45V

PolyPhen 2 Score 0.700 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000121621
Gene: ENSMUSG00000052581
AA Change: I45V

DomainStartEndE-ValueType
signal peptide 1 31 N/A INTRINSIC
LRRNT 34 66 1.66e0 SMART
LRR_TYP 85 108 6.67e-2 SMART
LRR 109 132 3.52e-1 SMART
LRR_TYP 133 156 2.53e-2 SMART
LRR 157 180 1.16e-1 SMART
LRR 181 204 4.34e-1 SMART
LRR 205 225 2.4e1 SMART
LRR 229 252 4.97e0 SMART
LRR 253 276 1.07e0 SMART
LRR 277 300 1.64e-1 SMART
Blast:LRRCT 312 362 4e-25 BLAST
low complexity region 376 393 N/A INTRINSIC
transmembrane domain 426 448 N/A INTRINSIC
low complexity region 465 470 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000145407
AA Change: I44V

PolyPhen 2 Score 0.505 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000114465
Gene: ENSMUSG00000052581
AA Change: I44V

DomainStartEndE-ValueType
signal peptide 1 30 N/A INTRINSIC
LRRNT 33 65 1.66e0 SMART
Blast:LRR_TYP 84 104 3e-7 BLAST
Predicted Effect possibly damaging
Transcript: ENSMUST00000147663
AA Change: I45V

PolyPhen 2 Score 0.700 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000117263
Gene: ENSMUSG00000052581
AA Change: I45V

DomainStartEndE-ValueType
signal peptide 1 31 N/A INTRINSIC
LRRNT 34 66 1.66e0 SMART
LRR_TYP 85 108 6.67e-2 SMART
LRR 109 132 3.52e-1 SMART
LRR_TYP 133 156 2.53e-2 SMART
LRR 157 180 1.16e-1 SMART
LRR 181 204 4.34e-1 SMART
LRR 205 225 2.4e1 SMART
LRR 229 252 4.97e0 SMART
LRR 253 276 1.07e0 SMART
LRR 277 300 1.64e-1 SMART
Blast:LRRCT 312 362 2e-25 BLAST
low complexity region 376 393 N/A INTRINSIC
transmembrane domain 426 448 N/A INTRINSIC
low complexity region 465 470 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.1%
  • 20x: 94.4%
Validation Efficiency
MGI Phenotype PHENOTYPE: Mice homozygous for a knock-out allele exhibit impaired excitatory synapse development and excitatory transmission in dentate gyrus granule cells. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930590J08Rik A T 6: 91,896,096 (GRCm39) R315W probably damaging Het
Atrn A T 2: 130,775,356 (GRCm39) Y153F possibly damaging Het
C4b A G 17: 34,948,167 (GRCm39) V1644A probably damaging Het
Carmil3 A C 14: 55,736,397 (GRCm39) K654T probably damaging Het
Cdh1 T C 8: 107,392,964 (GRCm39) probably null Het
Chrna1 C T 2: 73,398,444 (GRCm39) V332M probably benign Het
Clca3a2 A C 3: 144,797,886 (GRCm39) V193G possibly damaging Het
Cyld A G 8: 89,456,470 (GRCm39) probably null Het
Dbt A T 3: 116,317,074 (GRCm39) E83D possibly damaging Het
Deup1 T C 9: 15,472,618 (GRCm39) R471G possibly damaging Het
Dgcr2 T A 16: 17,675,173 (GRCm39) I188F possibly damaging Het
Dgkg G A 16: 22,376,788 (GRCm39) R524* probably null Het
Dnaaf9 G A 2: 130,656,109 (GRCm39) T2M probably damaging Het
Dnah5 A T 15: 28,453,425 (GRCm39) R4399W probably damaging Het
Egflam G A 15: 7,273,338 (GRCm39) T579I possibly damaging Het
Eif2b2 C T 12: 85,269,561 (GRCm39) T211I probably damaging Het
Ep400 A G 5: 110,883,386 (GRCm39) probably benign Het
Ermp1 C G 19: 29,593,129 (GRCm39) A788P probably benign Het
Ern1 A G 11: 106,317,699 (GRCm39) S142P possibly damaging Het
Fbxo15 T A 18: 84,999,250 (GRCm39) C351S probably damaging Het
Fndc3a A T 14: 72,806,307 (GRCm39) S444T probably benign Het
Gabra6 G A 11: 42,198,268 (GRCm39) T384M probably benign Het
Gpbp1l1 T C 4: 116,447,457 (GRCm39) V379A probably benign Het
Hook2 G T 8: 85,722,375 (GRCm39) E305* probably null Het
Hoxa3 G A 6: 52,149,568 (GRCm39) A21V probably damaging Het
Hs1bp3 C A 12: 8,391,915 (GRCm39) P339Q probably benign Het
Igha T A 12: 113,223,710 (GRCm39) T49S probably benign Het
Klra4 C T 6: 130,030,016 (GRCm39) V190M possibly damaging Het
Lats2 A G 14: 57,933,588 (GRCm39) L843P probably damaging Het
Lcmt1 A G 7: 123,020,839 (GRCm39) T255A probably benign Het
Lpar6 A G 14: 73,476,368 (GRCm39) I110V probably damaging Het
Mcm3ap T C 10: 76,307,000 (GRCm39) V371A probably benign Het
Muc20 A T 16: 32,614,944 (GRCm39) D144E possibly damaging Het
Nphp3 T A 9: 103,897,945 (GRCm39) D417E probably damaging Het
Or7g33 A T 9: 19,448,629 (GRCm39) I199K probably benign Het
Or8b40 A G 9: 38,027,670 (GRCm39) I193V probably benign Het
Paqr7 A C 4: 134,235,031 (GRCm39) Y296S probably damaging Het
Pcdha4 A T 18: 37,087,808 (GRCm39) T664S probably damaging Het
Pelo T A 13: 115,225,379 (GRCm39) Y282F probably benign Het
Plxna2 A T 1: 194,493,178 (GRCm39) I1818F probably damaging Het
Pnkd A G 1: 74,389,833 (GRCm39) D319G probably benign Het
Pnma8a C A 7: 16,694,809 (GRCm39) N221K probably benign Het
Ppp1cb T A 5: 32,640,810 (GRCm39) probably null Het
Prkca T G 11: 107,905,136 (GRCm39) I201L probably benign Het
Prp2rt A G 13: 97,235,705 (GRCm39) L14S probably benign Het
Rfx2 G A 17: 57,087,778 (GRCm39) R538C probably damaging Het
Rph3a T C 5: 121,101,936 (GRCm39) Q100R probably damaging Het
Rtel1 C T 2: 180,972,608 (GRCm39) R29* probably null Het
Scel T A 14: 103,843,060 (GRCm39) Y547* probably null Het
Sp100 C T 1: 85,606,804 (GRCm39) P303L probably damaging Het
Stk31 A G 6: 49,446,236 (GRCm39) S958G probably benign Het
Syne2 T A 12: 76,055,639 (GRCm39) V4168E probably benign Het
Tenm3 A T 8: 49,099,533 (GRCm39) S91T probably benign Het
Tmcc2 TTGCTGCTGCTGCTGCTGC TTGCTGCTGCTGCTGC 1: 132,285,493 (GRCm39) probably benign Het
Tmem248 T A 5: 130,258,349 (GRCm39) I14N probably damaging Het
Tor3a T C 1: 156,484,057 (GRCm39) I298V probably benign Het
Trim69 A T 2: 122,009,075 (GRCm39) K378N probably damaging Het
Ttc28 C T 5: 111,232,975 (GRCm39) P151S possibly damaging Het
Uaca T C 9: 60,779,294 (GRCm39) V1225A probably damaging Het
Vps4b T C 1: 106,705,065 (GRCm39) I343V probably benign Het
Wnk4 A G 11: 101,152,047 (GRCm39) T184A probably damaging Het
Ythdc2 T A 18: 45,006,023 (GRCm39) I1172K possibly damaging Het
Other mutations in Lrrtm4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00498:Lrrtm4 APN 6 79,999,529 (GRCm39) missense probably damaging 1.00
IGL02043:Lrrtm4 APN 6 79,998,845 (GRCm39) missense possibly damaging 0.89
IGL02603:Lrrtm4 APN 6 79,999,967 (GRCm39) missense possibly damaging 0.92
IGL02614:Lrrtm4 APN 6 79,998,827 (GRCm39) missense probably benign 0.01
IGL02735:Lrrtm4 APN 6 80,786,031 (GRCm39) missense probably benign
IGL02812:Lrrtm4 APN 6 79,998,947 (GRCm39) missense probably damaging 1.00
IGL02885:Lrrtm4 APN 6 79,998,786 (GRCm39) missense probably damaging 1.00
IGL02956:Lrrtm4 APN 6 79,998,633 (GRCm39) missense probably benign 0.04
IGL03242:Lrrtm4 APN 6 79,999,071 (GRCm39) missense probably benign 0.22
R0504:Lrrtm4 UTSW 6 79,999,029 (GRCm39) missense probably damaging 1.00
R0537:Lrrtm4 UTSW 6 79,999,103 (GRCm39) missense probably benign 0.02
R0656:Lrrtm4 UTSW 6 79,998,953 (GRCm39) missense possibly damaging 0.87
R0698:Lrrtm4 UTSW 6 79,999,911 (GRCm39) missense probably damaging 1.00
R1651:Lrrtm4 UTSW 6 79,999,511 (GRCm39) missense probably benign 0.06
R2126:Lrrtm4 UTSW 6 79,998,722 (GRCm39) missense probably damaging 1.00
R2211:Lrrtm4 UTSW 6 79,999,623 (GRCm39) missense probably benign 0.00
R2363:Lrrtm4 UTSW 6 79,998,857 (GRCm39) missense probably damaging 1.00
R3732:Lrrtm4 UTSW 6 79,996,638 (GRCm39) intron probably benign
R3817:Lrrtm4 UTSW 6 79,999,044 (GRCm39) missense probably benign 0.00
R4814:Lrrtm4 UTSW 6 80,000,117 (GRCm39) missense possibly damaging 0.69
R5304:Lrrtm4 UTSW 6 79,999,683 (GRCm39) missense probably benign 0.01
R5318:Lrrtm4 UTSW 6 79,999,495 (GRCm39) missense probably damaging 1.00
R5327:Lrrtm4 UTSW 6 79,999,620 (GRCm39) missense probably damaging 1.00
R6195:Lrrtm4 UTSW 6 79,998,939 (GRCm39) missense probably damaging 1.00
R7597:Lrrtm4 UTSW 6 79,999,428 (GRCm39) nonsense probably null
R7793:Lrrtm4 UTSW 6 79,999,841 (GRCm39) missense probably damaging 0.97
R7875:Lrrtm4 UTSW 6 79,999,343 (GRCm39) missense possibly damaging 0.89
R8058:Lrrtm4 UTSW 6 79,999,528 (GRCm39) missense probably benign
R8238:Lrrtm4 UTSW 6 79,999,668 (GRCm39) missense probably damaging 0.97
R8324:Lrrtm4 UTSW 6 79,998,974 (GRCm39) missense probably damaging 1.00
R8751:Lrrtm4 UTSW 6 79,999,092 (GRCm39) missense probably damaging 1.00
R8859:Lrrtm4 UTSW 6 79,998,870 (GRCm39) missense probably damaging 1.00
R9142:Lrrtm4 UTSW 6 79,999,426 (GRCm39) missense probably damaging 1.00
R9633:Lrrtm4 UTSW 6 80,000,064 (GRCm39) missense probably damaging 1.00
R9709:Lrrtm4 UTSW 6 80,786,154 (GRCm39) missense probably damaging 0.96
Z1177:Lrrtm4 UTSW 6 79,999,700 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- TGACACCCCTAATCTGGACG -3'
(R):5'- CCCTTGAAAGGCATCTTCGTC -3'

Sequencing Primer
(F):5'- CTAATCTGGACGAGCCTGTG -3'
(R):5'- TGAAAGGCATCTTCGTCCACTGAG -3'
Posted On 2017-02-28