Incidental Mutation 'R0735:Lat2'
ID68224
Institutional Source Beutler Lab
Gene Symbol Lat2
Ensembl Gene ENSMUSG00000040751
Gene Namelinker for activation of T cells family, member 2
SynonymsWbscr15, Wbscr5
MMRRC Submission 038916-MU
Accession Numbers
Is this an essential gene? Probably non essential (E-score: 0.060) question?
Stock #R0735 (G1)
Quality Score113
Status Validated
Chromosome5
Chromosomal Location134600022-134615025 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to C at 134606783 bp
ZygosityHeterozygous
Amino Acid Change Tyrosine to Cysteine at position 59 (Y59C)
Ref Sequence ENSEMBL: ENSMUSP00000143977 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023867] [ENSMUST00000036362] [ENSMUST00000077636] [ENSMUST00000200737] [ENSMUST00000200998] [ENSMUST00000202085]
Predicted Effect probably benign
Transcript: ENSMUST00000023867
SMART Domains Protein: ENSMUSP00000023867
Gene: ENSMUSG00000023104

DomainStartEndE-ValueType
AAA 63 189 9.42e-13 SMART
Pfam:Rep_fac_C 253 338 3.1e-19 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000036362
AA Change: Y59C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000046900
Gene: ENSMUSG00000040751
AA Change: Y59C

DomainStartEndE-ValueType
low complexity region 4 25 N/A INTRINSIC
Pfam:LAT2 29 197 6.6e-82 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000077636
AA Change: Y59C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000076824
Gene: ENSMUSG00000040751
AA Change: Y59C

DomainStartEndE-ValueType
signal peptide 1 29 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000200737
AA Change: Y59C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000143998
Gene: ENSMUSG00000040751
AA Change: Y59C

DomainStartEndE-ValueType
transmembrane domain 5 27 N/A INTRINSIC
Pfam:LAT2 29 114 9.5e-22 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000200945
Predicted Effect probably damaging
Transcript: ENSMUST00000200998
AA Change: Y59C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000143977
Gene: ENSMUSG00000040751
AA Change: Y59C

DomainStartEndE-ValueType
low complexity region 4 25 N/A INTRINSIC
Pfam:LAT2 29 197 6.6e-82 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000201632
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201832
Predicted Effect probably damaging
Transcript: ENSMUST00000202085
AA Change: Y59C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000144611
Gene: ENSMUSG00000040751
AA Change: Y59C

DomainStartEndE-ValueType
transmembrane domain 5 27 N/A INTRINSIC
Pfam:LAT2 29 116 7.5e-29 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000202461
Predicted Effect noncoding transcript
Transcript: ENSMUST00000202746
Meta Mutation Damage Score 0.6382 question?
Coding Region Coverage
  • 1x: 99.5%
  • 3x: 98.7%
  • 10x: 96.7%
  • 20x: 91.8%
Validation Efficiency 95% (73/77)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is one of the contiguous genes at 7q11.23 commonly deleted in Williams syndrome, a multisystem developmental disorder. This gene consists of at least 14 exons, and its alternative splicing generates 3 transcript variants, all encoding the same protein. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele have abnormal mast cell physiology and increased anti-nuclear antigen antibody level. Mice homozygous for another null allele show abnormal mast cell physiology, hyperactivated T cells, higher cytokine production, spleenhyperplasia and increased autoantibody level. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9930021J03Rik A T 19: 29,717,638 I1552K possibly damaging Het
Actr8 T A 14: 29,989,712 M405K probably benign Het
Adam10 G A 9: 70,748,251 V334I possibly damaging Het
Adgra2 G T 8: 27,117,318 G686C probably damaging Het
Akap11 A T 14: 78,510,078 I1623N probably damaging Het
Astn1 A T 1: 158,472,389 T100S possibly damaging Het
B3galt1 A C 2: 68,118,579 I213L possibly damaging Het
B4galnt4 A G 7: 141,064,323 K101E probably benign Het
Camsap2 A G 1: 136,292,888 S324P probably damaging Het
Chrnb4 A G 9: 55,043,800 S60P probably damaging Het
Cpne1 A G 2: 156,078,750 probably null Het
Cubn G A 2: 13,491,689 probably benign Het
Cul7 T A 17: 46,663,190 L1467H probably damaging Het
Cxcl15 T C 5: 90,801,294 M106T probably benign Het
Cyp2c23 A T 19: 44,016,810 M140K probably damaging Het
Dgke A G 11: 89,060,075 F104S probably benign Het
Dhx36 T A 3: 62,472,729 M849L probably benign Het
Dnah7a C T 1: 53,544,511 E1522K possibly damaging Het
Edil3 G T 13: 89,177,178 V219F probably damaging Het
Egln1 A G 8: 124,948,495 V187A possibly damaging Het
Fam193a T C 5: 34,439,378 I455T possibly damaging Het
Fdft1 A T 14: 63,163,420 I88N probably damaging Het
Fem1c G A 18: 46,505,160 R592C probably benign Het
Frs2 T A 10: 117,074,582 S292C probably damaging Het
Gm15448 T C 7: 3,821,782 T533A possibly damaging Het
Gpr107 T A 2: 31,171,994 F145I probably benign Het
Gpr153 T A 4: 152,279,373 C83* probably null Het
H2-Q7 T G 17: 35,440,186 probably null Het
Hsp90b1 A T 10: 86,695,748 probably benign Het
Kcnk1 C A 8: 126,025,289 N211K probably damaging Het
Klb T C 5: 65,379,727 V800A probably benign Het
Mlkl A T 8: 111,327,801 probably benign Het
Mroh2a G A 1: 88,243,950 R770Q probably damaging Het
Mtbp T A 15: 55,562,942 C93* probably null Het
Myo7a A G 7: 98,081,180 probably benign Het
Myt1 G A 2: 181,807,387 probably benign Het
Ogfrl1 T C 1: 23,375,754 Q224R possibly damaging Het
Olfr418 A G 1: 173,271,002 T276A probably benign Het
Olfr661 A T 7: 104,688,819 H268L probably damaging Het
Osbpl2 A G 2: 180,150,290 probably benign Het
Plb1 C T 5: 32,284,920 T252M possibly damaging Het
Ptpro T A 6: 137,443,594 V1007D probably damaging Het
Rbsn T C 6: 92,189,693 T657A probably benign Het
Rims4 C T 2: 163,863,929 V262M possibly damaging Het
Rps6kb2 C A 19: 4,157,883 S348I probably benign Het
Rsrp1 C T 4: 134,924,257 R111W unknown Het
Ryr3 T C 2: 112,732,982 T2933A probably benign Het
Scara5 A G 14: 65,731,019 D247G possibly damaging Het
Slc7a11 C T 3: 50,424,096 S231N probably benign Het
Sod2 A T 17: 13,010,564 N91Y probably damaging Het
Spesp1 A T 9: 62,272,685 S314T probably benign Het
St3gal1 C A 15: 67,113,687 M39I probably benign Het
Stat6 A T 10: 127,658,241 I646F probably damaging Het
Tdrd1 A T 19: 56,865,978 K1119* probably null Het
Thbs2 A G 17: 14,679,815 I600T probably benign Het
Tor1a A G 2: 30,963,838 V160A probably damaging Het
Trdmt1 T G 2: 13,523,438 D104A probably benign Het
Trim58 T C 11: 58,651,393 V393A probably benign Het
Trip4 C T 9: 65,884,918 probably benign Het
Trip6 T C 5: 137,310,821 E341G probably benign Het
Ttn T A 2: 76,715,195 I32595F probably damaging Het
Ubr4 T A 4: 139,428,028 probably null Het
Ush2a G A 1: 188,864,693 V3877I probably benign Het
Vmn1r29 G T 6: 58,307,732 G146C probably damaging Het
Vmn2r53 A G 7: 12,581,780 V704A probably benign Het
Vmn2r7 C T 3: 64,716,367 M268I probably benign Het
Wnt7b G A 15: 85,537,495 T248M probably damaging Het
Xab2 G A 8: 3,613,649 P394S possibly damaging Het
Zfp663 A G 2: 165,359,075 V13A probably damaging Het
Other mutations in Lat2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00482:Lat2 APN 5 134606776 critical splice donor site probably null
IGL01897:Lat2 APN 5 134606627 splice site probably benign
IGL02869:Lat2 APN 5 134608173 missense probably damaging 1.00
IGL03018:Lat2 APN 5 134602591 missense probably damaging 0.97
R1739:Lat2 UTSW 5 134606369 missense possibly damaging 0.93
R2257:Lat2 UTSW 5 134602627 missense probably damaging 1.00
R2866:Lat2 UTSW 5 134605944 missense probably damaging 0.99
R4675:Lat2 UTSW 5 134606057 missense probably damaging 0.99
R5008:Lat2 UTSW 5 134603137 missense probably benign 0.02
R6014:Lat2 UTSW 5 134603454 missense probably damaging 1.00
R6422:Lat2 UTSW 5 134603161 missense probably benign 0.00
R7330:Lat2 UTSW 5 134606787 missense probably damaging 0.99
R7512:Lat2 UTSW 5 134605944 missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- TCACTTACCCTCAAGGTGGGAGAAC -3'
(R):5'- ACAGACAGACACATTTCTATGCTCAGC -3'

Sequencing Primer
(F):5'- ACATAGTGAGGTCTAGCCCTG -3'
(R):5'- gacacatttctatgctcagctCTTC -3'
Posted On2013-09-03