Incidental Mutation 'R4675:Lat2'
ID 349475
Institutional Source Beutler Lab
Gene Symbol Lat2
Ensembl Gene ENSMUSG00000040751
Gene Name linker for activation of T cells family, member 2
Synonyms Wbscr5, Wbscr15
MMRRC Submission 041930-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.050) question?
Stock # R4675 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 134628876-134643879 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 134634911 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 100 (N100S)
Ref Sequence ENSEMBL: ENSMUSP00000143977 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023867] [ENSMUST00000036362] [ENSMUST00000077636] [ENSMUST00000200737] [ENSMUST00000200998] [ENSMUST00000202085]
AlphaFold Q9JHL0
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: N100S

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000046900
Gene: ENSMUSG00000040751
AA Change: N100S

DomainStartEndE-ValueType
low complexity region 4 25 N/A INTRINSIC
Pfam:LAT2 29 197 6.6e-82 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000077636
SMART Domains Protein: ENSMUSP00000076824
Gene: ENSMUSG00000040751

DomainStartEndE-ValueType
signal peptide 1 29 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000200737
SMART Domains Protein: ENSMUSP00000143998
Gene: ENSMUSG00000040751

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: N100S

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000143977
Gene: ENSMUSG00000040751
AA Change: N100S

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 possibly damaging
Transcript: ENSMUST00000202085
AA Change: N104S

PolyPhen 2 Score 0.707 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000144611
Gene: ENSMUSG00000040751
AA Change: N104S

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201832
Meta Mutation Damage Score 0.0780 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.9%
Validation Efficiency 95% (89/94)
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: 88 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310061I04Rik C A 17: 36,203,820 (GRCm39) K291N probably damaging Het
Adgra1 A G 7: 139,456,102 (GRCm39) T577A probably damaging Het
Akip1 T A 7: 109,308,188 (GRCm39) I152N possibly damaging Het
Armc9 A G 1: 86,130,240 (GRCm39) Y8C probably damaging Het
Atp1a4 A T 1: 172,085,223 (GRCm39) V66E possibly damaging Het
Atp2a3 A T 11: 72,872,623 (GRCm39) T724S probably damaging Het
Bmp1 C A 14: 70,730,284 (GRCm39) R416L probably damaging Het
Bmt2 G T 6: 13,663,300 (GRCm39) A66E probably benign Het
Bscl2 A T 19: 8,825,523 (GRCm39) D403V possibly damaging Het
Cbx2 T A 11: 118,919,935 (GRCm39) I500N probably damaging Het
Cd84 A T 1: 171,700,887 (GRCm39) H216L possibly damaging Het
Cdhr18 A T 14: 13,856,724 (GRCm38) D462E probably benign Het
Ceacam15 T C 7: 16,407,410 (GRCm39) T36A probably benign Het
Cebpd A G 16: 15,705,385 (GRCm39) D66G probably damaging Het
Cntnap4 A G 8: 113,512,468 (GRCm39) Y610C probably damaging Het
Col11a2 T C 17: 34,283,267 (GRCm39) probably null Het
Col17a1 T C 19: 47,651,497 (GRCm39) probably null Het
Cracr2b A G 7: 141,043,451 (GRCm39) D43G probably damaging Het
Dgkz T A 2: 91,768,691 (GRCm39) K697* probably null Het
Dnah7b T A 1: 46,256,317 (GRCm39) D1873E possibly damaging Het
Dst G A 1: 34,314,784 (GRCm39) E6472K possibly damaging Het
Duox2 T C 2: 122,111,414 (GRCm39) D1428G probably damaging Het
Elmod2 T C 8: 84,043,537 (GRCm39) N210S probably damaging Het
Ephx1 A G 1: 180,822,256 (GRCm39) F220S probably damaging Het
F13b A G 1: 139,429,542 (GRCm39) Y20C unknown Het
Fbn2 T A 18: 58,173,265 (GRCm39) N2051I possibly damaging Het
Gabrg2 G A 11: 41,859,650 (GRCm39) H201Y probably damaging Het
Gbgt1 T C 2: 28,388,453 (GRCm39) F46S possibly damaging Het
Gjd4 A G 18: 9,280,578 (GRCm39) S167P probably damaging Het
Heatr5a T C 12: 51,924,130 (GRCm39) N2028D probably benign Het
Heca T C 10: 17,791,057 (GRCm39) H333R probably benign Het
Herc1 T C 9: 66,298,740 (GRCm39) S625P probably damaging Het
Ighv1-55 T C 12: 115,172,175 (GRCm39) probably benign Het
Ighv5-8 G A 12: 113,618,777 (GRCm39) S64N probably benign Het
Itga1 G T 13: 115,138,227 (GRCm39) probably null Het
Kif21a C A 15: 90,824,748 (GRCm39) R1342L possibly damaging Het
Ksr1 G A 11: 78,965,186 (GRCm39) P118S possibly damaging Het
Lrit3 T A 3: 129,582,121 (GRCm39) D501V probably damaging Het
Lrrfip1 T A 1: 91,031,042 (GRCm39) probably null Het
Lyst G A 13: 13,809,968 (GRCm39) R546H probably damaging Het
Med21 T A 6: 146,551,691 (GRCm39) L114H probably damaging Het
Mfap4 A T 11: 61,376,336 (GRCm39) probably benign Het
Mpdz G A 4: 81,302,049 (GRCm39) R233W probably damaging Het
Mrc2 G A 11: 105,239,257 (GRCm39) probably null Het
Ncapd3 T C 9: 27,006,038 (GRCm39) probably benign Het
Neto2 T G 8: 86,396,333 (GRCm39) H104P probably damaging Het
Nr1h2 T C 7: 44,201,979 (GRCm39) T36A possibly damaging Het
Nudt16l2 T C 9: 105,021,647 (GRCm39) D133G probably benign Het
Or13a20 A T 7: 140,232,074 (GRCm39) M61L probably damaging Het
Or4a79 T C 2: 89,551,838 (GRCm39) I206V probably benign Het
Or51ab3 T G 7: 103,201,183 (GRCm39) L64V probably damaging Het
Or51g2 A G 7: 102,623,013 (GRCm39) M62T probably damaging Het
Or52p1 T A 7: 104,267,631 (GRCm39) C248* probably null Het
Or5p52 A G 7: 107,502,567 (GRCm39) I214M probably damaging Het
Or5p72 T C 7: 108,022,309 (GRCm39) V177A possibly damaging Het
Or8b4 T C 9: 37,830,882 (GRCm39) *310R probably null Het
Pcbp3 A G 10: 76,606,869 (GRCm39) L241S possibly damaging Het
Pcf11 G A 7: 92,308,985 (GRCm39) probably benign Het
Podxl G A 6: 31,503,579 (GRCm39) T254M possibly damaging Het
Prr27 A C 5: 87,991,100 (GRCm39) E237D possibly damaging Het
Rdh16 G T 10: 127,637,316 (GRCm39) V84F probably damaging Het
Rnf26 A T 9: 44,023,428 (GRCm39) D273E probably benign Het
Rpl13a A T 7: 44,776,242 (GRCm39) probably benign Het
Rpl3l A G 17: 24,952,584 (GRCm39) K239E probably benign Het
Rsf1 G A 7: 97,229,117 (GRCm39) probably benign Het
Rsf1 A AGGGCGACGG 7: 97,229,111 (GRCm39) probably null Het
Ryk A G 9: 102,768,415 (GRCm39) D352G possibly damaging Het
Setd1b T A 5: 123,299,061 (GRCm39) probably benign Het
Sh2b1 G A 7: 126,070,618 (GRCm39) A361V possibly damaging Het
Slc35f3 A T 8: 127,047,935 (GRCm39) K92* probably null Het
Slc39a10 A G 1: 46,857,144 (GRCm39) probably benign Het
Slc47a1 G A 11: 61,253,857 (GRCm39) T194I probably benign Het
Slc6a3 C A 13: 73,692,936 (GRCm39) N185K probably damaging Het
Stag1 T C 9: 100,730,758 (GRCm39) V391A probably damaging Het
Syne2 A C 12: 75,996,075 (GRCm39) N2206T probably damaging Het
Tbc1d23 C A 16: 57,003,325 (GRCm39) R481I possibly damaging Het
Tcstv7b T C 13: 120,702,362 (GRCm39) W53R probably damaging Het
Tfam A G 10: 71,069,225 (GRCm39) S166P probably benign Het
Tmem63a A G 1: 180,784,056 (GRCm39) H212R probably benign Het
Txndc11 T A 16: 10,902,745 (GRCm39) Q634L possibly damaging Het
Usp31 T C 7: 121,306,548 (GRCm39) probably benign Het
Vmn1r204 A T 13: 22,740,962 (GRCm39) M198L probably damaging Het
Vmn2r17 A T 5: 109,575,049 (GRCm39) T119S probably benign Het
Vsig1 A G X: 139,833,861 (GRCm39) D227G probably damaging Het
Zfhx2 G A 14: 55,304,678 (GRCm39) P1102L probably benign Het
Zfp715 T C 7: 42,949,444 (GRCm39) Q172R probably benign Het
Zfp872 A G 9: 22,108,701 (GRCm39) D53G probably damaging Het
Zswim8 G A 14: 20,764,681 (GRCm39) D684N probably benign Het
Other mutations in Lat2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00482:Lat2 APN 5 134,635,630 (GRCm39) critical splice donor site probably null
IGL01897:Lat2 APN 5 134,635,481 (GRCm39) splice site probably benign
IGL02869:Lat2 APN 5 134,637,027 (GRCm39) missense probably damaging 1.00
IGL03018:Lat2 APN 5 134,631,445 (GRCm39) missense probably damaging 0.97
R0735:Lat2 UTSW 5 134,635,637 (GRCm39) missense probably damaging 1.00
R1739:Lat2 UTSW 5 134,635,223 (GRCm39) missense possibly damaging 0.93
R2257:Lat2 UTSW 5 134,631,481 (GRCm39) missense probably damaging 1.00
R2866:Lat2 UTSW 5 134,634,798 (GRCm39) missense probably damaging 0.99
R5008:Lat2 UTSW 5 134,631,991 (GRCm39) missense probably benign 0.02
R6014:Lat2 UTSW 5 134,632,308 (GRCm39) missense probably damaging 1.00
R6422:Lat2 UTSW 5 134,632,015 (GRCm39) missense probably benign 0.00
R7330:Lat2 UTSW 5 134,635,641 (GRCm39) missense probably damaging 0.99
R7512:Lat2 UTSW 5 134,634,798 (GRCm39) missense probably damaging 0.99
R8811:Lat2 UTSW 5 134,635,553 (GRCm39) intron probably benign
Predicted Primers PCR Primer
(F):5'- CACCAGATTGAAAGGCTGCTC -3'
(R):5'- CAAAGGTCTGGCCATTCAAAG -3'

Sequencing Primer
(F):5'- GAAGCAGTCTTCACTTAATGCC -3'
(R):5'- GGCCATTCAAAGCCCCTAGG -3'
Posted On 2015-10-08