Incidental Mutation 'R4246:Lrfn1'
ID 320425
Institutional Source Beutler Lab
Gene Symbol Lrfn1
Ensembl Gene ENSMUSG00000030600
Gene Name leucine rich repeat and fibronectin type III domain containing 1
Synonyms SALM2
MMRRC Submission 041062-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.342) question?
Stock # R4246 (G1)
Quality Score 225
Status Not validated
Chromosome 7
Chromosomal Location 28151405-28167667 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 28159367 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Leucine at position 429 (V429L)
Ref Sequence ENSEMBL: ENSMUSP00000139609 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000040531] [ENSMUST00000055110] [ENSMUST00000108288] [ENSMUST00000189877] [ENSMUST00000190954]
AlphaFold Q2WF71
Predicted Effect probably benign
Transcript: ENSMUST00000040531
SMART Domains Protein: ENSMUSP00000040486
Gene: ENSMUSG00000109336

DomainStartEndE-ValueType
low complexity region 81 90 N/A INTRINSIC
low complexity region 174 190 N/A INTRINSIC
low complexity region 200 211 N/A INTRINSIC
low complexity region 278 290 N/A INTRINSIC
SAM 296 359 1.02e-9 SMART
low complexity region 406 420 N/A INTRINSIC
low complexity region 433 461 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000055110
AA Change: V429L

PolyPhen 2 Score 0.031 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000057645
Gene: ENSMUSG00000030600
AA Change: V429L

DomainStartEndE-ValueType
low complexity region 2 28 N/A INTRINSIC
LRR 88 111 8.67e-1 SMART
LRR 112 135 4.57e0 SMART
LRR_TYP 136 159 1.69e-3 SMART
LRR 161 184 2.54e1 SMART
LRR 185 208 2.32e-1 SMART
LRR 209 233 3.75e0 SMART
LRRCT 252 297 1.36e-3 SMART
IGc2 312 377 1.51e-12 SMART
low complexity region 389 403 N/A INTRINSIC
low complexity region 460 471 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000108288
AA Change: V429L

PolyPhen 2 Score 0.031 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000103923
Gene: ENSMUSG00000030600
AA Change: V429L

DomainStartEndE-ValueType
low complexity region 2 28 N/A INTRINSIC
LRR 88 111 8.67e-1 SMART
LRR 112 135 4.57e0 SMART
LRR_TYP 136 159 1.69e-3 SMART
LRR 161 184 2.54e1 SMART
LRR 185 208 2.32e-1 SMART
LRR 209 233 3.75e0 SMART
LRRCT 252 297 1.36e-3 SMART
IGc2 312 377 1.51e-12 SMART
low complexity region 389 403 N/A INTRINSIC
FN3 422 502 2.68e-2 SMART
transmembrane domain 535 557 N/A INTRINSIC
low complexity region 589 601 N/A INTRINSIC
low complexity region 609 625 N/A INTRINSIC
low complexity region 716 725 N/A INTRINSIC
low complexity region 730 747 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000189877
AA Change: V429L

PolyPhen 2 Score 0.031 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000139609
Gene: ENSMUSG00000030600
AA Change: V429L

DomainStartEndE-ValueType
low complexity region 2 28 N/A INTRINSIC
LRR 88 111 8.67e-1 SMART
LRR 112 135 4.57e0 SMART
LRR_TYP 136 159 1.69e-3 SMART
LRR 161 184 2.54e1 SMART
LRR 185 208 2.32e-1 SMART
LRR 209 233 3.75e0 SMART
LRRCT 252 297 1.36e-3 SMART
IGc2 312 377 1.51e-12 SMART
low complexity region 389 403 N/A INTRINSIC
low complexity region 460 471 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000190954
SMART Domains Protein: ENSMUSP00000140537
Gene: ENSMUSG00000030600

DomainStartEndE-ValueType
signal peptide 1 31 N/A INTRINSIC
Blast:LRRNT 33 69 2e-18 BLAST
LRR 88 111 3.7e-3 SMART
LRR 112 135 1.9e-2 SMART
LRR_TYP 136 159 7.1e-6 SMART
LRR 161 184 1.1e-1 SMART
LRR 185 208 1e-3 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000191267
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.9%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2700062C07Rik A G 18: 24,606,013 (GRCm39) N36S possibly damaging Het
Ak1 A G 2: 32,523,384 (GRCm39) T151A possibly damaging Het
Asxl3 A G 18: 22,658,557 (GRCm39) D2189G probably damaging Het
Ccdc91 C T 6: 147,493,646 (GRCm39) A346V unknown Het
Dnah6 C T 6: 73,106,431 (GRCm39) E1769K probably benign Het
Dock6 A T 9: 21,750,786 (GRCm39) probably null Het
Fhod3 A G 18: 25,123,123 (GRCm39) K271R probably null Het
Glyatl3 T A 17: 41,220,989 (GRCm39) D126V probably benign Het
Gnal C G 18: 67,221,654 (GRCm39) P19R unknown Het
Igkv8-21 T A 6: 70,292,436 (GRCm39) M1L possibly damaging Het
Itih4 C A 14: 30,613,359 (GRCm39) H261N probably damaging Het
Jpt1 T C 11: 115,405,119 (GRCm39) probably benign Het
Kif14 G T 1: 136,401,126 (GRCm39) M492I possibly damaging Het
Klhl32 A C 4: 24,800,822 (GRCm39) S3A possibly damaging Het
Kmt2d C T 15: 98,737,970 (GRCm39) probably benign Het
Lamtor5 T C 3: 107,186,354 (GRCm39) V41A probably benign Het
Lmtk3 G A 7: 45,443,486 (GRCm39) C723Y possibly damaging Het
Mapkbp1 T A 2: 119,843,508 (GRCm39) I252N probably damaging Het
Nelfa A G 5: 34,056,373 (GRCm39) F464S probably damaging Het
Nipbl G A 15: 8,361,916 (GRCm39) L1454F probably damaging Het
Nr4a3 C T 4: 48,083,125 (GRCm39) P553S possibly damaging Het
Nrg3 G A 14: 39,194,198 (GRCm39) T187I possibly damaging Het
Or5m5 T A 2: 85,814,624 (GRCm39) C147S possibly damaging Het
Or8g36 A G 9: 39,422,899 (GRCm39) V39A probably benign Het
Pcdha8 A G 18: 37,125,950 (GRCm39) E144G probably damaging Het
Pik3cb T C 9: 98,983,229 (GRCm39) probably null Het
Pira1 C T 7: 3,740,348 (GRCm39) G291E probably damaging Het
Pkd1l1 C T 11: 8,815,543 (GRCm39) R1456K possibly damaging Het
Ppp1r3a T A 6: 14,719,780 (GRCm39) E378V probably damaging Het
Psd2 T C 18: 36,139,172 (GRCm39) L540P probably damaging Het
Rnf14 T A 18: 38,434,701 (GRCm39) probably null Het
Satl1 A G X: 111,316,033 (GRCm39) S141P probably benign Het
Setx GTGGCT GT 2: 29,044,073 (GRCm39) 1814 probably null Het
Sh3d19 G A 3: 86,033,995 (GRCm39) V783I probably benign Het
Snca T C 6: 60,710,149 (GRCm39) E110G possibly damaging Het
Sumf1 A C 6: 108,131,974 (GRCm39) V156G probably damaging Het
Trhr A T 15: 44,096,856 (GRCm39) probably null Het
Tsen2 A G 6: 115,524,785 (GRCm39) probably benign Het
Tuft1 C A 3: 94,522,108 (GRCm39) M319I probably benign Het
Vill C A 9: 118,889,461 (GRCm39) N132K probably damaging Het
Wars2 T A 3: 99,123,904 (GRCm39) V255E probably damaging Het
Zcchc14 CTGATGGTGGTGGTGATGGTGGTGG CTGATGGTGGTGG 8: 122,331,031 (GRCm39) probably benign Het
Other mutations in Lrfn1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00494:Lrfn1 APN 7 28,159,442 (GRCm39) missense probably damaging 1.00
IGL01565:Lrfn1 APN 7 28,158,194 (GRCm39) missense probably damaging 1.00
IGL01622:Lrfn1 APN 7 28,166,111 (GRCm39) missense probably damaging 1.00
IGL01623:Lrfn1 APN 7 28,166,111 (GRCm39) missense probably damaging 1.00
IGL02176:Lrfn1 APN 7 28,158,111 (GRCm39) intron probably benign
IGL02642:Lrfn1 APN 7 28,158,113 (GRCm39) intron probably benign
R1123:Lrfn1 UTSW 7 28,166,544 (GRCm39) missense possibly damaging 0.71
R1838:Lrfn1 UTSW 7 28,159,193 (GRCm39) missense probably damaging 0.98
R3000:Lrfn1 UTSW 7 28,166,832 (GRCm39) missense probably damaging 1.00
R3551:Lrfn1 UTSW 7 28,159,479 (GRCm39) missense possibly damaging 0.90
R3905:Lrfn1 UTSW 7 28,166,294 (GRCm39) missense possibly damaging 0.49
R5621:Lrfn1 UTSW 7 28,166,261 (GRCm39) missense probably damaging 1.00
R6267:Lrfn1 UTSW 7 28,159,169 (GRCm39) missense probably benign 0.01
R6902:Lrfn1 UTSW 7 28,159,238 (GRCm39) missense probably benign 0.10
R7059:Lrfn1 UTSW 7 28,166,355 (GRCm39) missense possibly damaging 0.65
R7073:Lrfn1 UTSW 7 28,159,397 (GRCm39) missense possibly damaging 0.94
R7208:Lrfn1 UTSW 7 28,166,564 (GRCm39) missense probably benign
R7402:Lrfn1 UTSW 7 28,158,947 (GRCm39) missense probably damaging 1.00
R8378:Lrfn1 UTSW 7 28,159,157 (GRCm39) missense probably benign 0.26
R8791:Lrfn1 UTSW 7 28,159,344 (GRCm39) missense probably benign 0.00
R8870:Lrfn1 UTSW 7 28,158,918 (GRCm39) missense possibly damaging 0.71
R9452:Lrfn1 UTSW 7 28,159,157 (GRCm39) missense probably damaging 1.00
R9483:Lrfn1 UTSW 7 28,158,183 (GRCm39) missense probably damaging 1.00
R9579:Lrfn1 UTSW 7 28,166,769 (GRCm39) missense probably damaging 1.00
R9649:Lrfn1 UTSW 7 28,166,255 (GRCm39) missense probably damaging 1.00
Z1176:Lrfn1 UTSW 7 28,158,540 (GRCm39) missense possibly damaging 0.66
Predicted Primers PCR Primer
(F):5'- TTGCATAGCCTCCAATGCTGC -3'
(R):5'- AGCTGGAACTAAGCAAGGTC -3'

Sequencing Primer
(F):5'- TCCAATGCTGCGGGGGAAG -3'
(R):5'- CTGGAACTAAGCAAGGTCAAGGG -3'
Posted On 2015-06-12