Incidental Mutation 'R3841:Lrrc4c'
ID 277145
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 040781-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.099) question?
Stock # R3841 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 96148514-97462011 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 97460537 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 388 (T388A)
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: T388A

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000131795
Gene: ENSMUSG00000050587
AA Change: T388A

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: T388A

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000130984
Gene: ENSMUSG00000050587
AA Change: T388A

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: T388A

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000125218
Gene: ENSMUSG00000050587
AA Change: T388A

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 0.1185 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.2%
Validation Efficiency 98% (43/44)
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: 43 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4921524L21Rik A T 18: 6,620,104 (GRCm39) K11N probably benign Het
Atp8b3 A G 10: 80,365,540 (GRCm39) F405L possibly damaging Het
BC035947 G T 1: 78,474,482 (GRCm39) N683K probably benign Het
Bmper T A 9: 23,384,727 (GRCm39) probably null Het
Btnl7-ps A G 17: 34,761,550 (GRCm39) noncoding transcript Het
Cmya5 A G 13: 93,231,140 (GRCm39) V1316A probably damaging Het
Cracd A T 5: 77,006,858 (GRCm39) Q1073L unknown Het
Dgcr6 C A 16: 17,888,077 (GRCm39) Y200* probably null Het
Dsp A C 13: 38,381,681 (GRCm39) I2210L probably benign Het
Eef1e1 G A 13: 38,840,167 (GRCm39) T46I probably damaging Het
Epc2 A G 2: 49,378,750 (GRCm39) K68R probably damaging Het
F11r G T 1: 171,288,457 (GRCm39) R100L probably damaging Het
Fam83c C T 2: 155,676,668 (GRCm39) R34H probably benign Het
Fbxw25 A T 9: 109,491,202 (GRCm39) Y105* probably null Het
Ggt1 T A 10: 75,417,219 (GRCm39) Y5* probably null Het
Hipk2 T C 6: 38,795,861 (GRCm39) E136G probably damaging Het
Hsph1 T A 5: 149,544,180 (GRCm39) probably null Het
Impdh1 A G 6: 29,202,768 (GRCm39) S421P probably damaging Het
Jhy T A 9: 40,856,142 (GRCm39) E115V probably benign Het
Kmt2a T C 9: 44,742,588 (GRCm39) probably benign Het
Ldlrap1 T C 4: 134,477,747 (GRCm39) T159A probably damaging Het
Map3k10 C A 7: 27,357,789 (GRCm39) C663F possibly damaging Het
Me3 A T 7: 89,435,701 (GRCm39) N179Y possibly damaging Het
Medag T A 5: 149,350,888 (GRCm39) I121N probably damaging Het
Mocos C T 18: 24,809,681 (GRCm39) A428V probably damaging Het
Mok C T 12: 110,781,591 (GRCm39) V59M probably benign Het
Neb C A 2: 52,097,672 (GRCm39) probably null Het
Nr2c2 C T 6: 92,140,119 (GRCm39) R464W probably damaging Het
Or52s1 G A 7: 102,861,900 (GRCm39) G267R probably damaging Het
Or6c35 A G 10: 129,169,202 (GRCm39) I151V probably benign Het
Otud1 G T 2: 19,663,554 (GRCm39) E228* probably null Het
Parp4 A T 14: 56,825,235 (GRCm39) N120Y probably damaging Het
Ptprb T C 10: 116,182,887 (GRCm39) V1521A possibly damaging Het
Rap1gap T C 4: 137,444,758 (GRCm39) F182S probably damaging Het
Rcan2 A G 17: 44,347,870 (GRCm39) K193R probably benign Het
Rdh19 A T 10: 127,692,755 (GRCm39) M141L probably benign Het
Selenok C T 14: 29,695,337 (GRCm39) R72* probably null Het
Tbpl1 A G 10: 22,587,807 (GRCm39) probably benign Het
Tnxb A G 17: 34,917,897 (GRCm39) E2270G possibly damaging Het
Tulp1 A G 17: 28,572,689 (GRCm39) V489A probably damaging Het
Utp20 A T 10: 88,611,065 (GRCm39) probably benign Het
Zfp617 G A 8: 72,685,961 (GRCm39) G97E probably damaging Het
Zfp773 A G 7: 7,135,390 (GRCm39) V402A possibly damaging 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
R3552:Lrrc4c UTSW 2 97,460,306 (GRCm39) missense probably damaging 1.00
R3840: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'- TGGATAAGAGACATGGCCCC -3'
(R):5'- TGGTTGCCGCAGTAACATTC -3'

Sequencing Primer
(F):5'- TGTGCCAGGTGTAACACTC -3'
(R):5'- TTGCCGCAGTAACATTCAAGGTG -3'
Posted On 2015-04-06