Incidental Mutation 'IGL02869:Lat2'
ID 362474
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Lat2
Ensembl Gene ENSMUSG00000040751
Gene Name linker for activation of T cells family, member 2
Synonyms Wbscr5, Wbscr15
Accession Numbers
Essential gene? Probably non essential (E-score: 0.050) question?
Stock # IGL02869
Quality Score
Status
Chromosome 5
Chromosomal Location 134628876-134643879 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 134637027 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 40 (I40T)
Ref Sequence ENSEMBL: ENSMUSP00000143977 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000036362] [ENSMUST00000077636] [ENSMUST00000200737] [ENSMUST00000200998] [ENSMUST00000202085]
AlphaFold Q9JHL0
Predicted Effect probably damaging
Transcript: ENSMUST00000036362
AA Change: I40T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000046900
Gene: ENSMUSG00000040751
AA Change: I40T

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: I40T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000076824
Gene: ENSMUSG00000040751
AA Change: I40T

DomainStartEndE-ValueType
signal peptide 1 29 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000200737
AA Change: I40T

PolyPhen 2 Score 0.931 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000143998
Gene: ENSMUSG00000040751
AA Change: I40T

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: I40T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000143977
Gene: ENSMUSG00000040751
AA Change: I40T

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: I40T

PolyPhen 2 Score 0.931 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000144611
Gene: ENSMUSG00000040751
AA Change: I40T

DomainStartEndE-ValueType
transmembrane domain 5 27 N/A INTRINSIC
Pfam:LAT2 29 116 7.5e-29 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201832
Predicted Effect noncoding transcript
Transcript: ENSMUST00000202461
Predicted Effect noncoding transcript
Transcript: ENSMUST00000202746
Coding Region Coverage
Validation Efficiency
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: 95 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930562C15Rik T A 16: 4,685,323 (GRCm39) S1142T possibly damaging Het
Aadacl4fm5 T C 4: 144,512,938 (GRCm39) I54V probably benign Het
Actr3b T G 5: 26,037,433 (GRCm39) V215G probably damaging Het
Adam9 C T 8: 25,460,634 (GRCm39) V617M probably damaging Het
Adgrl2 G T 3: 148,596,241 (GRCm39) P32T probably damaging Het
Afg2a G T 3: 37,518,694 (GRCm39) G743W probably damaging Het
Ago3 A T 4: 126,261,580 (GRCm39) probably benign Het
Allc A C 12: 28,623,206 (GRCm39) I20M probably benign Het
Asic3 G A 5: 24,621,972 (GRCm39) W361* probably null Het
Atf7ip A G 6: 136,583,577 (GRCm39) K1203E probably damaging Het
Babam2 C A 5: 32,162,116 (GRCm39) H272Q possibly damaging Het
Baz2b G A 2: 59,807,872 (GRCm39) T129I probably benign Het
C130073F10Rik A T 4: 101,747,590 (GRCm39) Y146* probably null Het
Cd247 A G 1: 165,684,986 (GRCm39) E74G probably damaging Het
Cdh17 A T 4: 11,814,908 (GRCm39) Q778L probably benign Het
Ceacam1 T C 7: 25,175,966 (GRCm39) D76G probably benign Het
Cela3a T C 4: 137,131,145 (GRCm39) K198E probably benign Het
Cemip2 T A 19: 21,789,241 (GRCm39) D558E probably damaging Het
Ces2a T A 8: 105,465,691 (GRCm39) D281E probably damaging Het
Cetn2 A T X: 71,958,527 (GRCm39) D116E probably damaging Het
Cracd A G 5: 77,006,890 (GRCm39) K1084E unknown Het
Ctu2 G T 8: 123,205,530 (GRCm39) probably null Het
Cybb T C X: 9,308,828 (GRCm39) N469D probably benign Het
Cygb C T 11: 116,540,749 (GRCm39) R79Q probably damaging Het
Cyp2d10 C T 15: 82,288,069 (GRCm39) V186M possibly damaging Het
Defb29 T A 2: 152,380,942 (GRCm39) probably null Het
Depdc7 T G 2: 104,560,694 (GRCm39) Q100P probably damaging Het
Dhx30 A C 9: 109,926,251 (GRCm39) I91R probably damaging Het
Dnm1l T A 16: 16,159,288 (GRCm39) K105* probably null Het
Eddm13 T C 7: 6,272,898 (GRCm39) probably benign Het
Efhc1 T C 1: 21,037,567 (GRCm39) I248T probably damaging Het
Elapor1 A G 3: 108,380,182 (GRCm39) I309T probably benign Het
Entpd2 A G 2: 25,288,120 (GRCm39) T115A probably damaging Het
Epb42 G T 2: 120,856,227 (GRCm39) A439E probably benign Het
Esm1 T G 13: 113,346,618 (GRCm39) L81R probably damaging Het
F8 T C X: 74,330,987 (GRCm39) S968G probably benign Het
Fam234b T G 6: 135,202,201 (GRCm39) Y308D probably damaging Het
Fbxo46 T G 7: 18,871,139 (GRCm39) V586G probably damaging Het
Foxp1 C A 6: 98,907,044 (GRCm39) probably benign Het
Gm10754 A T 10: 97,518,136 (GRCm39) probably benign Het
Gm12695 A C 4: 96,650,370 (GRCm39) probably benign Het
Gm5468 T C 15: 25,414,726 (GRCm39) probably benign Het
Grhl1 T C 12: 24,631,490 (GRCm39) S66P probably damaging Het
Gstt3 A T 10: 75,612,576 (GRCm39) probably null Het
Gtf2i A G 5: 134,308,281 (GRCm39) probably benign Het
Gzmk C A 13: 113,308,560 (GRCm39) G175C probably damaging Het
Helz2 T C 2: 180,872,939 (GRCm39) probably benign Het
Ift20 T C 11: 78,430,780 (GRCm39) probably benign Het
Intu A G 3: 40,642,216 (GRCm39) D491G probably damaging Het
Itch G T 2: 155,015,853 (GRCm39) probably null Het
Itgb5 A G 16: 33,665,362 (GRCm39) N26S possibly damaging Het
Lama2 A T 10: 26,891,534 (GRCm39) S2526R probably damaging Het
Lipa T A 19: 34,471,397 (GRCm39) M393L probably benign Het
Lipa G T 19: 34,471,371 (GRCm39) probably benign Het
Lpcat1 T A 13: 73,632,417 (GRCm39) L10H probably damaging Het
Lpcat3 T C 6: 124,679,970 (GRCm39) Y348H possibly damaging Het
Lrp1b A T 2: 40,591,842 (GRCm39) N50K unknown Het
Lrrk2 T A 15: 91,634,480 (GRCm39) Y1415N probably damaging Het
Lsamp A T 16: 41,965,078 (GRCm39) T312S probably benign Het
Man2a2 T C 7: 80,013,689 (GRCm39) E454G probably benign Het
Mcm3 T C 1: 20,879,063 (GRCm39) K570R probably damaging Het
Mctp2 C A 7: 71,878,219 (GRCm39) probably null Het
Msantd2 T G 9: 37,434,796 (GRCm39) C345W probably damaging Het
Musk T C 4: 58,354,078 (GRCm39) I362T probably benign Het
Myh15 A T 16: 48,965,767 (GRCm39) N1224I probably benign Het
Myo18a A G 11: 77,755,612 (GRCm39) Y1983C probably damaging Het
Myo18a C T 11: 77,720,699 (GRCm39) probably benign Het
Myrfl G T 10: 116,664,909 (GRCm39) Q374K probably damaging Het
Ndrg1 T A 15: 66,818,346 (GRCm39) Q87H probably benign Het
Nol9 G A 4: 152,131,030 (GRCm39) C351Y probably damaging Het
Nr5a1 A G 2: 38,598,141 (GRCm39) S219P probably benign Het
Or8b43 T C 9: 38,360,489 (GRCm39) F107S possibly damaging Het
Or8g28 A T 9: 39,169,520 (GRCm39) Y149* probably null Het
Pcdhb19 A G 18: 37,631,690 (GRCm39) D495G probably damaging Het
Pfkm A G 15: 98,026,123 (GRCm39) M573V probably damaging Het
Plec A T 15: 76,065,516 (GRCm39) L1586Q probably damaging Het
Prelp C A 1: 133,843,005 (GRCm39) E47* probably null Het
Rbm33 T A 5: 28,615,753 (GRCm39) I32N probably damaging Het
Rgs12 A T 5: 35,183,227 (GRCm39) D310V probably damaging Het
Ripor2 A C 13: 24,880,512 (GRCm39) H404P possibly damaging Het
Sh3d21 T C 4: 126,056,034 (GRCm39) E124G probably benign Het
Shroom2 C T X: 151,442,549 (GRCm39) S872N probably benign Het
Slc44a5 A G 3: 153,956,651 (GRCm39) Y301C probably damaging Het
Smap1 A T 1: 23,930,995 (GRCm39) H66Q possibly damaging Het
Smyd1 G T 6: 71,198,007 (GRCm39) probably benign Het
Sptbn4 T A 7: 27,093,573 (GRCm39) probably benign Het
Srsf3-ps T A 11: 98,516,146 (GRCm39) R76* probably null Het
Stag3 A G 5: 138,280,955 (GRCm39) K49R probably damaging Het
Stim1 C A 7: 101,917,758 (GRCm39) A46E unknown Het
Stxbp2 A T 8: 3,691,971 (GRCm39) I538F probably benign Het
Tbc1d19 A G 5: 53,992,559 (GRCm39) T114A probably benign Het
Tln2 G A 9: 67,128,807 (GRCm39) probably benign Het
Trmt10a T A 3: 137,857,945 (GRCm39) probably null Het
Vwde G A 6: 13,187,136 (GRCm39) H784Y probably damaging Het
Zfp773 T C 7: 7,137,232 (GRCm39) T121A 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
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
R4675:Lat2 UTSW 5 134,634,911 (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
Posted On 2015-12-18