Incidental Mutation 'R3552:Lrrc4c'
ID 268973
Institutional Source Beutler Lab
Gene Symbol Lrrc4c
Ensembl Gene ENSMUSG00000050587
Gene Name leucine rich repeat containing 4C
Synonyms 6430556C10Rik, netrin g1 ligand, NGL-1
MMRRC Submission 040669-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.099) question?
Stock # R3552 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 96148514-97462011 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 97460306 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tryptophan to Arginine at position 311 (W311R)
Ref Sequence ENSEMBL: ENSMUSP00000125218 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000059049] [ENSMUST00000135431] [ENSMUST00000162807] [ENSMUST00000170144]
AlphaFold Q8C031
Predicted Effect probably damaging
Transcript: ENSMUST00000059049
AA Change: W311R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000131795
Gene: ENSMUSG00000050587
AA Change: W311R

DomainStartEndE-ValueType
low complexity region 26 42 N/A INTRINSIC
LRRNT 46 80 6.95e-4 SMART
LRR 79 98 1.97e2 SMART
LRR_TYP 99 122 7.37e-4 SMART
LRR 123 146 1.08e-1 SMART
LRR_TYP 147 170 1.38e-3 SMART
Blast:LRR 171 195 5e-8 BLAST
LRR 196 217 8.03e1 SMART
LRR_TYP 218 241 2.12e-4 SMART
LRR 242 265 6.97e1 SMART
LRR_TYP 266 289 2.53e-2 SMART
LRRCT 301 352 2.68e-2 SMART
IGc2 366 433 1.22e-7 SMART
transmembrane domain 526 548 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000135431
AA Change: W311R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000130984
Gene: ENSMUSG00000050587
AA Change: W311R

DomainStartEndE-ValueType
low complexity region 26 42 N/A INTRINSIC
LRRNT 46 80 6.95e-4 SMART
LRR 79 98 1.97e2 SMART
LRR_TYP 99 122 7.37e-4 SMART
LRR 123 146 1.08e-1 SMART
LRR_TYP 147 170 1.38e-3 SMART
Blast:LRR 171 195 5e-8 BLAST
LRR 196 217 8.03e1 SMART
LRR_TYP 218 241 2.12e-4 SMART
LRR 242 265 6.97e1 SMART
LRR_TYP 266 289 2.53e-2 SMART
LRRCT 301 352 2.68e-2 SMART
IGc2 366 433 1.22e-7 SMART
transmembrane domain 526 548 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000162807
AA Change: W311R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000125218
Gene: ENSMUSG00000050587
AA Change: W311R

DomainStartEndE-ValueType
low complexity region 26 42 N/A INTRINSIC
LRRNT 46 80 6.95e-4 SMART
LRR 79 98 1.97e2 SMART
LRR_TYP 99 122 7.37e-4 SMART
LRR 123 146 1.08e-1 SMART
LRR_TYP 147 170 1.38e-3 SMART
Blast:LRR 171 195 5e-8 BLAST
LRR 196 217 8.03e1 SMART
LRR_TYP 218 241 2.12e-4 SMART
LRR 242 265 6.97e1 SMART
LRR_TYP 266 289 2.53e-2 SMART
LRRCT 301 352 2.68e-2 SMART
IGc2 366 433 1.22e-7 SMART
transmembrane domain 526 548 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000170144
Predicted Effect noncoding transcript
Transcript: ENSMUST00000199276
Meta Mutation Damage Score 0.9510 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 93.4%
Validation Efficiency 100% (66/66)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] NGL1 is a specific binding partner for netrin G1 (NTNG1; MIM 608818), which is a member of the netrin family of axon guidance molecules (Lin et al., 2003 [PubMed 14595443]).[supplied by OMIM, Mar 2008]
PHENOTYPE: Homozygous mutant mice exhibited an increased mean serum IL-6 response to LPS challenge when compared with controls. No other notable phenotype was detected in a high-througput screen. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acaca T A 11: 84,152,450 (GRCm39) Y866N probably damaging Het
Agk A G 6: 40,371,615 (GRCm39) T371A probably benign Het
Akna T C 4: 63,316,361 (GRCm39) M1V probably null Het
Aldh7a1 T C 18: 56,683,364 (GRCm39) probably null Het
Ankrd26 A T 6: 118,484,737 (GRCm39) L1500H probably damaging Het
Atp13a5 T A 16: 29,129,584 (GRCm39) D452V probably damaging Het
Bahcc1 C T 11: 120,167,598 (GRCm39) T1333M possibly damaging Het
Carmil3 G T 14: 55,744,859 (GRCm39) R1276L possibly damaging Het
Ccni T C 5: 93,335,620 (GRCm39) S173G probably benign Het
Chrm2 A T 6: 36,500,745 (GRCm39) I201F probably damaging Het
Col16a1 A G 4: 129,970,834 (GRCm39) T618A probably benign Het
Dele1 A G 18: 38,391,418 (GRCm39) probably benign Het
Dock2 T C 11: 34,611,787 (GRCm39) Y192C probably benign Het
Ep400 T A 5: 110,877,153 (GRCm39) E821V unknown Het
Esrrg G A 1: 187,882,387 (GRCm39) V215I probably benign Het
Evx1 A T 6: 52,293,908 (GRCm39) S359C probably damaging Het
Fcrl2 A G 3: 87,166,717 (GRCm39) I92T possibly damaging Het
Gal3st1 T A 11: 3,948,110 (GRCm39) F106I possibly damaging Het
Gm9944 T C 4: 144,179,613 (GRCm39) probably benign Het
Hjurp GT GTT 1: 88,194,246 (GRCm39) probably null Het
Hrc G C 7: 44,985,757 (GRCm39) E303Q possibly damaging Het
Kcnh1 A G 1: 191,921,074 (GRCm39) N118D probably damaging Het
Khdrbs1 A G 4: 129,614,584 (GRCm39) I323T possibly damaging Het
Klhdc7b T C 15: 89,271,724 (GRCm39) Y869H probably benign Het
Megf11 A G 9: 64,602,745 (GRCm39) D862G possibly damaging Het
Muc5b A G 7: 141,415,072 (GRCm39) T2673A possibly damaging Het
Muc5b A G 7: 141,421,442 (GRCm39) S4311G probably benign Het
Myo15a C T 11: 60,400,489 (GRCm39) A1767V possibly damaging Het
Neo1 T A 9: 58,801,161 (GRCm39) K1140M probably damaging Het
Oc90 T C 15: 65,750,650 (GRCm39) Q365R possibly damaging Het
Oplah C T 15: 76,186,294 (GRCm39) D734N possibly damaging Het
Or1e19 T C 11: 73,316,678 (GRCm39) I44V probably benign Het
Or4c58 A C 2: 89,674,687 (GRCm39) M210R possibly damaging Het
Or9g3 T C 2: 85,590,237 (GRCm39) N161S possibly damaging Het
Pbx1 G A 1: 167,986,362 (GRCm39) P411L possibly damaging Het
Pcdhga6 G T 18: 37,841,270 (GRCm39) R330L probably benign Het
Phox2b C A 5: 67,254,999 (GRCm39) R150L probably damaging Het
Plscr2 A G 9: 92,172,848 (GRCm39) E169G probably damaging Het
Ptprn2 A T 12: 116,852,497 (GRCm39) Q518L probably benign Het
Rbl1 A T 2: 157,037,505 (GRCm39) I214K probably benign Het
Ryr1 T A 7: 28,756,422 (GRCm39) Q3464L probably damaging Het
Ryr3 T A 2: 112,582,132 (GRCm39) I2854F probably damaging Het
Shtn1 T C 19: 58,963,470 (GRCm39) Y615C probably benign Het
Sirt5 A T 13: 43,536,643 (GRCm39) N226Y probably damaging Het
Slc30a3 G A 5: 31,252,422 (GRCm39) probably benign Het
Slc5a4b A G 10: 75,917,358 (GRCm39) V226A probably damaging Het
Slf2 C A 19: 44,923,390 (GRCm39) S68* probably null Het
Smyd5 G A 6: 85,419,193 (GRCm39) E292K probably damaging Het
Spns1 A G 7: 125,969,543 (GRCm39) V512A possibly damaging Het
Sry T A Y: 2,663,141 (GRCm39) Q173L unknown Het
Ssrp1 C A 2: 84,874,736 (GRCm39) Q519K probably benign Het
Tgfbr3 T C 5: 107,287,705 (GRCm39) E498G probably damaging Het
Tnrc6b T G 15: 80,764,448 (GRCm39) L650W probably damaging Het
Tnxb A T 17: 34,937,695 (GRCm39) E3861D probably damaging Het
Trbc1 G T 6: 41,516,579 (GRCm39) probably benign Het
Trpm7 T A 2: 126,668,630 (GRCm39) probably benign Het
Usp39 G A 6: 72,314,815 (GRCm39) T197I possibly damaging Het
Vmn1r38 T C 6: 66,753,477 (GRCm39) H213R possibly damaging Het
Washc2 A G 6: 116,197,529 (GRCm39) D168G probably damaging Het
Washc4 A G 10: 83,382,720 (GRCm39) I45V probably benign Het
Zfp352 A G 4: 90,113,339 (GRCm39) E493G probably benign Het
Zfp692 C T 11: 58,200,254 (GRCm39) T170I possibly damaging Het
Zfp735 C A 11: 73,602,067 (GRCm39) S337* probably null Het
Other mutations in Lrrc4c
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00482:Lrrc4c APN 2 97,460,730 (GRCm39) nonsense probably null
IGL02095:Lrrc4c APN 2 97,459,749 (GRCm39) missense probably benign 0.05
IGL02165:Lrrc4c APN 2 97,459,378 (GRCm39) start codon destroyed probably null 0.33
IGL02176:Lrrc4c APN 2 97,460,598 (GRCm39) missense probably damaging 0.96
IGL02674:Lrrc4c APN 2 97,460,120 (GRCm39) missense probably damaging 0.99
IGL03082:Lrrc4c APN 2 97,460,931 (GRCm39) missense probably benign 0.05
IGL03303:Lrrc4c APN 2 97,459,937 (GRCm39) missense probably damaging 1.00
R0946:Lrrc4c UTSW 2 97,459,809 (GRCm39) missense probably benign 0.00
R1037:Lrrc4c UTSW 2 97,460,330 (GRCm39) missense probably benign
R1518:Lrrc4c UTSW 2 97,460,921 (GRCm39) missense probably benign
R1559:Lrrc4c UTSW 2 97,461,117 (GRCm39) missense probably benign 0.00
R2192:Lrrc4c UTSW 2 97,459,657 (GRCm39) missense possibly damaging 0.50
R2213:Lrrc4c UTSW 2 97,460,816 (GRCm39) missense probably benign 0.29
R2279:Lrrc4c UTSW 2 97,460,850 (GRCm39) missense possibly damaging 0.86
R3840:Lrrc4c UTSW 2 97,460,537 (GRCm39) missense probably damaging 0.98
R3841:Lrrc4c UTSW 2 97,460,537 (GRCm39) missense probably damaging 0.98
R4606:Lrrc4c UTSW 2 97,460,658 (GRCm39) missense probably benign 0.22
R4938:Lrrc4c UTSW 2 97,459,646 (GRCm39) missense probably damaging 1.00
R4946:Lrrc4c UTSW 2 97,460,834 (GRCm39) missense probably benign 0.00
R5323:Lrrc4c UTSW 2 97,460,498 (GRCm39) missense probably damaging 1.00
R6014:Lrrc4c UTSW 2 97,459,557 (GRCm39) splice site probably null
R6297:Lrrc4c UTSW 2 97,459,964 (GRCm39) missense probably damaging 0.99
R6376:Lrrc4c UTSW 2 97,459,391 (GRCm39) missense probably benign 0.03
R7032:Lrrc4c UTSW 2 97,459,410 (GRCm39) missense probably benign
R7419:Lrrc4c UTSW 2 97,460,106 (GRCm39) missense probably benign 0.07
R7699:Lrrc4c UTSW 2 97,461,024 (GRCm39) missense possibly damaging 0.81
R7700:Lrrc4c UTSW 2 97,461,024 (GRCm39) missense possibly damaging 0.81
R7723:Lrrc4c UTSW 2 97,460,999 (GRCm39) missense possibly damaging 0.91
R7736:Lrrc4c UTSW 2 97,460,705 (GRCm39) missense probably benign 0.02
R7843:Lrrc4c UTSW 2 97,460,558 (GRCm39) missense probably benign 0.19
R7880:Lrrc4c UTSW 2 97,461,143 (GRCm39) missense probably benign 0.08
R8008:Lrrc4c UTSW 2 97,460,594 (GRCm39) missense possibly damaging 0.88
R8479:Lrrc4c UTSW 2 97,459,977 (GRCm39) missense probably damaging 1.00
R8802:Lrrc4c UTSW 2 97,460,603 (GRCm39) missense possibly damaging 0.83
R8821:Lrrc4c UTSW 2 97,460,040 (GRCm39) missense possibly damaging 0.88
R8906:Lrrc4c UTSW 2 97,460,393 (GRCm39) missense probably benign 0.00
R8933:Lrrc4c UTSW 2 97,459,826 (GRCm39) missense probably benign 0.36
R8974:Lrrc4c UTSW 2 97,459,992 (GRCm39) missense probably damaging 1.00
R9115:Lrrc4c UTSW 2 97,459,686 (GRCm39) missense probably benign 0.00
R9266:Lrrc4c UTSW 2 97,459,853 (GRCm39) missense probably benign 0.26
R9311:Lrrc4c UTSW 2 97,461,080 (GRCm39) missense possibly damaging 0.90
Z1177:Lrrc4c UTSW 2 97,460,828 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- AATCAGGCCTGGCTCTTTTC -3'
(R):5'- AGTGACATTGAGGTCTGCAGG -3'

Sequencing Primer
(F):5'- GGGTTGATGCACCTTCAAAAACTG -3'
(R):5'- TGCAGGGGGCTCCACAATTAC -3'
Posted On 2015-02-19