Incidental Mutation 'R0492:Lct'
ID 42510
Institutional Source Beutler Lab
Gene Symbol Lct
Ensembl Gene ENSMUSG00000026354
Gene Name lactase
Synonyms LPH, LOC226413, Lphl
MMRRC Submission 038690-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0492 (G1)
Quality Score 225
Status Validated
Chromosome 1
Chromosomal Location 128212493-128256055 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 128228319 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 1058 (D1058G)
Ref Sequence ENSEMBL: ENSMUSP00000073190 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000073490]
AlphaFold F8VPT3
Predicted Effect probably damaging
Transcript: ENSMUST00000073490
AA Change: D1058G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000073190
Gene: ENSMUSG00000026354
AA Change: D1058G

DomainStartEndE-ValueType
Pfam:Glyco_hydro_1 76 226 1.6e-19 PFAM
low complexity region 322 340 N/A INTRINSIC
Pfam:Glyco_hydro_1 380 849 4.8e-169 PFAM
low complexity region 865 875 N/A INTRINSIC
Pfam:Glyco_hydro_1 902 1368 3.7e-181 PFAM
Pfam:Glyco_hydro_1 1377 1844 6.9e-183 PFAM
transmembrane domain 1885 1907 N/A INTRINSIC
Meta Mutation Damage Score 0.7032 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.7%
  • 20x: 93.7%
Validation Efficiency 99% (99/100)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene belongs to the glycosyl hydrolase 1 family of proteins. The encoded preproprotein is proteolytically processed to generate the mature enzyme. This enzyme is integral to the plasma membrane and has both phlorizin hydrolase activity and lactase activity. Mutations in this gene are associated with congenital lactase deficiency. Polymorphisms in this gene are associated with lactase persistence, in which intestinal lactase activity persists at childhood levels into adulthood. [provided by RefSeq, Jan 2016]
Allele List at MGI
Other mutations in this stock
Total: 98 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrb2 C G 4: 129,901,624 (GRCm39) P416R probably damaging Het
Adgre1 A G 17: 57,709,742 (GRCm39) D133G unknown Het
Alpl A C 4: 137,476,887 (GRCm39) probably null Het
Ankrd65 T C 4: 155,875,133 (GRCm39) probably benign Het
Baalc A T 15: 38,797,480 (GRCm39) probably benign Het
Bpifb5 A G 2: 154,070,820 (GRCm39) T204A probably benign Het
Bud31 A G 5: 145,083,265 (GRCm39) Y77C probably damaging Het
Calhm6 G A 10: 34,003,647 (GRCm39) R87* probably null Het
Capsl A G 15: 9,461,930 (GRCm39) probably benign Het
Ccna1 A G 3: 54,956,004 (GRCm39) V116A probably damaging Het
Cdc42bpa C A 1: 179,928,755 (GRCm39) H723N probably benign Het
Cfap161 T C 7: 83,443,245 (GRCm39) I40V possibly damaging Het
CK137956 C T 4: 127,845,093 (GRCm39) V217I probably benign Het
Cog5 A G 12: 31,919,460 (GRCm39) T540A probably damaging Het
Cps1 T C 1: 67,196,995 (GRCm39) W349R probably damaging Het
Crispld2 G T 8: 120,752,806 (GRCm39) V285L probably benign Het
Crtc2 T A 3: 90,170,804 (GRCm39) F626I probably damaging Het
Daam1 G A 12: 71,991,154 (GRCm39) R256H unknown Het
Dhx38 G T 8: 110,288,576 (GRCm39) probably benign Het
Dok4 G A 8: 95,591,764 (GRCm39) A324V probably benign Het
Dscam T C 16: 96,626,982 (GRCm39) probably null Het
Dusp16 A T 6: 134,695,365 (GRCm39) S489T probably benign Het
Ecpas A G 4: 58,864,418 (GRCm39) W288R probably damaging Het
Erbin A T 13: 103,970,866 (GRCm39) Y917N probably damaging Het
F13b A T 1: 139,450,297 (GRCm39) probably null Het
Fdx1 C A 9: 51,874,725 (GRCm39) A15S probably benign Het
Ffar4 A T 19: 38,085,630 (GRCm39) Q19L probably benign Het
Folh1 A C 7: 86,395,400 (GRCm39) V344G probably damaging Het
Fscb T A 12: 64,520,292 (GRCm39) E391D possibly damaging Het
Gigyf2 G A 1: 87,368,568 (GRCm39) G1083R probably damaging Het
Gm14403 C A 2: 177,200,359 (GRCm39) H102N probably benign Het
Gm4847 A G 1: 166,457,961 (GRCm39) F464S probably damaging Het
Gpam A T 19: 55,084,611 (GRCm39) M56K possibly damaging Het
Gpr165 T A X: 95,760,778 (GRCm39) F352I probably damaging Het
Grik2 T G 10: 48,977,260 (GRCm39) I891L probably damaging Het
Gsr T C 8: 34,171,603 (GRCm39) probably benign Het
Hhla1 A G 15: 65,808,140 (GRCm39) F302L probably benign Het
Impg1 T C 9: 80,252,590 (GRCm39) D453G possibly damaging Het
Inpp5d T A 1: 87,625,872 (GRCm39) V495E possibly damaging Het
Iqca1l A T 5: 24,759,626 (GRCm39) L48Q probably damaging Het
Iqce A T 5: 140,660,990 (GRCm39) L450H probably damaging Het
Itfg2 A G 6: 128,390,486 (GRCm39) probably null Het
Kif13a A G 13: 46,966,218 (GRCm39) V400A possibly damaging Het
Kif7 T C 7: 79,363,629 (GRCm39) Y93C probably damaging Het
Krt33a A G 11: 99,906,909 (GRCm39) V22A probably benign Het
Lrp6 G T 6: 134,457,481 (GRCm39) D774E possibly damaging Het
Lrrc9 T A 12: 72,525,537 (GRCm39) S828R possibly damaging Het
Ly75 A G 2: 60,138,620 (GRCm39) W1416R probably damaging Het
Mdh2 T C 5: 135,819,004 (GRCm39) I320T possibly damaging Het
Med13l T A 5: 118,876,560 (GRCm39) V912E probably damaging Het
Mgarp T C 3: 51,296,456 (GRCm39) D182G possibly damaging Het
Mllt10 T C 2: 18,151,698 (GRCm39) probably benign Het
Mmp28 G A 11: 83,334,629 (GRCm39) A375V probably damaging Het
Mrps23 T A 11: 88,101,511 (GRCm39) H133Q probably benign Het
Msh6 T C 17: 88,282,679 (GRCm39) S35P probably benign Het
Myo3a A G 2: 22,328,447 (GRCm39) D347G possibly damaging Het
Npc1l1 T C 11: 6,173,040 (GRCm39) K800E possibly damaging Het
Or2ag13 A T 7: 106,473,084 (GRCm39) Y123N probably damaging Het
Or51ai2 T C 7: 103,586,971 (GRCm39) I128T probably benign Het
Or5i1 T G 2: 87,613,166 (GRCm39) I94S probably damaging Het
Or5m9 T C 2: 85,876,931 (GRCm39) V35A probably benign Het
Or5m9 T C 2: 85,877,278 (GRCm39) F151L possibly damaging Het
Or5t7 G A 2: 86,506,834 (GRCm39) P281L probably damaging Het
Or6p1 T A 1: 174,258,129 (GRCm39) I45N possibly damaging Het
Osmr A C 15: 6,853,999 (GRCm39) W570G probably damaging Het
Otol1 A T 3: 69,935,117 (GRCm39) I370F probably damaging Het
Pank2 A G 2: 131,122,180 (GRCm39) Y235C probably damaging Het
Pias2 T C 18: 77,193,581 (GRCm39) S187P probably damaging Het
Pkhd1l1 A G 15: 44,383,086 (GRCm39) N1115S probably benign Het
Pld1 G T 3: 28,163,966 (GRCm39) A800S probably damaging Het
Prex2 T C 1: 11,256,857 (GRCm39) probably benign Het
Ptpn3 T C 4: 57,194,304 (GRCm39) Q908R probably benign Het
Rab3gap2 T A 1: 184,984,589 (GRCm39) probably benign Het
Rbm24 A T 13: 46,573,826 (GRCm39) N82Y probably damaging Het
Rpl27 T C 11: 101,336,081 (GRCm39) V47A possibly damaging Het
Serpina1f A G 12: 103,659,826 (GRCm39) V152A possibly damaging Het
Serpina5 A G 12: 104,068,392 (GRCm39) Y151C probably damaging Het
Serpinb7 A G 1: 107,379,737 (GRCm39) *381W probably null Het
Sh2b2 A G 5: 136,261,117 (GRCm39) F33S probably damaging Het
Slc22a2 A C 17: 12,834,159 (GRCm39) I476L probably benign Het
Slc6a12 A T 6: 121,332,331 (GRCm39) I222F probably benign Het
Smim26 G A 2: 144,437,033 (GRCm39) D61N probably damaging Het
Soat1 A T 1: 156,268,924 (GRCm39) Y209N probably benign Het
Sorl1 T C 9: 41,902,667 (GRCm39) H1630R probably null Het
Sptlc2 A T 12: 87,393,580 (GRCm39) probably null Het
Strn3 G A 12: 51,657,187 (GRCm39) T642I probably damaging Het
Syce1l T A 8: 114,380,700 (GRCm39) D137E possibly damaging Het
Syne2 T C 12: 76,028,837 (GRCm39) probably null Het
Tcf25 C A 8: 124,108,203 (GRCm39) P86Q probably benign Het
Tmem19 A T 10: 115,197,715 (GRCm39) Y43* probably null Het
Tmem30b T C 12: 73,592,942 (GRCm39) N58D probably benign Het
Tnn A C 1: 159,948,327 (GRCm39) I795M probably damaging Het
Tnpo1 A G 13: 98,991,954 (GRCm39) Y641H probably damaging Het
Tra2a A T 6: 49,227,889 (GRCm39) probably benign Het
Trappc8 A T 18: 20,999,243 (GRCm39) F295I probably benign Het
Vmn2r101 T A 17: 19,809,245 (GRCm39) W125R probably damaging Het
Vps8 C A 16: 21,261,107 (GRCm39) F82L probably damaging Het
Ythdf2 A T 4: 131,931,779 (GRCm39) S460R probably damaging Het
Other mutations in Lct
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00777:Lct APN 1 128,215,293 (GRCm39) missense probably benign 0.09
IGL00970:Lct APN 1 128,231,805 (GRCm39) missense probably damaging 1.00
IGL01022:Lct APN 1 128,228,596 (GRCm39) missense probably benign
IGL01878:Lct APN 1 128,222,003 (GRCm39) missense probably damaging 1.00
IGL01892:Lct APN 1 128,235,342 (GRCm39) missense probably damaging 1.00
IGL02307:Lct APN 1 128,214,327 (GRCm39) missense possibly damaging 0.70
IGL02434:Lct APN 1 128,231,527 (GRCm39) missense probably damaging 0.97
IGL02559:Lct APN 1 128,222,003 (GRCm39) missense probably damaging 1.00
IGL02623:Lct APN 1 128,235,988 (GRCm39) missense probably benign 0.01
IGL02818:Lct APN 1 128,227,905 (GRCm39) missense probably damaging 1.00
IGL02949:Lct APN 1 128,240,869 (GRCm39) missense probably benign 0.26
IGL02951:Lct APN 1 128,227,948 (GRCm39) missense probably damaging 1.00
IGL03087:Lct APN 1 128,228,112 (GRCm39) missense possibly damaging 0.81
IGL03227:Lct APN 1 128,255,426 (GRCm39) missense probably benign 0.09
ANU18:Lct UTSW 1 128,235,784 (GRCm39) nonsense probably null
R0071:Lct UTSW 1 128,219,755 (GRCm39) nonsense probably null
R0071:Lct UTSW 1 128,219,755 (GRCm39) nonsense probably null
R0135:Lct UTSW 1 128,212,860 (GRCm39) missense probably damaging 0.98
R0145:Lct UTSW 1 128,255,632 (GRCm39) missense probably benign 0.00
R0179:Lct UTSW 1 128,255,422 (GRCm39) missense probably benign
R0331:Lct UTSW 1 128,226,479 (GRCm39) splice site probably benign
R0366:Lct UTSW 1 128,214,199 (GRCm39) missense probably benign 0.03
R0399:Lct UTSW 1 128,228,262 (GRCm39) missense probably damaging 1.00
R0548:Lct UTSW 1 128,212,932 (GRCm39) missense probably damaging 1.00
R0691:Lct UTSW 1 128,235,971 (GRCm39) missense probably benign 0.00
R0755:Lct UTSW 1 128,221,872 (GRCm39) missense possibly damaging 0.46
R0839:Lct UTSW 1 128,214,346 (GRCm39) missense probably benign 0.00
R1128:Lct UTSW 1 128,229,046 (GRCm39) missense probably damaging 0.99
R1135:Lct UTSW 1 128,221,861 (GRCm39) critical splice donor site probably null
R1321:Lct UTSW 1 128,227,759 (GRCm39) missense probably benign
R1448:Lct UTSW 1 128,235,559 (GRCm39) missense probably damaging 0.99
R1450:Lct UTSW 1 128,235,640 (GRCm39) missense probably damaging 1.00
R1572:Lct UTSW 1 128,221,932 (GRCm39) missense probably benign 0.25
R1582:Lct UTSW 1 128,228,299 (GRCm39) missense probably damaging 1.00
R1668:Lct UTSW 1 128,215,459 (GRCm39) splice site probably null
R1757:Lct UTSW 1 128,228,994 (GRCm39) missense probably damaging 1.00
R1775:Lct UTSW 1 128,228,038 (GRCm39) missense probably damaging 1.00
R1792:Lct UTSW 1 128,255,679 (GRCm39) missense possibly damaging 0.54
R1815:Lct UTSW 1 128,227,896 (GRCm39) missense probably damaging 1.00
R1932:Lct UTSW 1 128,221,898 (GRCm39) missense probably damaging 1.00
R2325:Lct UTSW 1 128,231,963 (GRCm39) missense probably damaging 1.00
R2381:Lct UTSW 1 128,231,858 (GRCm39) nonsense probably null
R3001:Lct UTSW 1 128,231,963 (GRCm39) missense probably damaging 1.00
R3002:Lct UTSW 1 128,231,963 (GRCm39) missense probably damaging 1.00
R3003:Lct UTSW 1 128,231,963 (GRCm39) missense probably damaging 1.00
R3011:Lct UTSW 1 128,229,109 (GRCm39) missense possibly damaging 0.74
R3082:Lct UTSW 1 128,215,345 (GRCm39) missense probably damaging 1.00
R3683:Lct UTSW 1 128,231,963 (GRCm39) missense probably damaging 1.00
R3684:Lct UTSW 1 128,231,963 (GRCm39) missense probably damaging 1.00
R3726:Lct UTSW 1 128,231,963 (GRCm39) missense probably damaging 1.00
R3886:Lct UTSW 1 128,231,963 (GRCm39) missense probably damaging 1.00
R3887:Lct UTSW 1 128,231,963 (GRCm39) missense probably damaging 1.00
R3888:Lct UTSW 1 128,231,963 (GRCm39) missense probably damaging 1.00
R4019:Lct UTSW 1 128,231,963 (GRCm39) missense probably damaging 1.00
R4027:Lct UTSW 1 128,212,918 (GRCm39) missense probably benign 0.00
R4226:Lct UTSW 1 128,231,963 (GRCm39) missense probably damaging 1.00
R4409:Lct UTSW 1 128,231,963 (GRCm39) missense probably damaging 1.00
R4514:Lct UTSW 1 128,228,251 (GRCm39) missense probably benign
R4570:Lct UTSW 1 128,227,641 (GRCm39) missense probably benign 0.01
R4776:Lct UTSW 1 128,228,124 (GRCm39) missense probably damaging 0.99
R5001:Lct UTSW 1 128,235,978 (GRCm39) missense probably damaging 0.96
R5021:Lct UTSW 1 128,228,302 (GRCm39) missense probably benign 0.38
R5318:Lct UTSW 1 128,232,109 (GRCm39) missense probably damaging 1.00
R5330:Lct UTSW 1 128,226,266 (GRCm39) missense probably benign 0.06
R5385:Lct UTSW 1 128,239,354 (GRCm39) missense possibly damaging 0.63
R5499:Lct UTSW 1 128,214,414 (GRCm39) missense probably damaging 1.00
R5508:Lct UTSW 1 128,221,868 (GRCm39) missense probably damaging 1.00
R5642:Lct UTSW 1 128,222,969 (GRCm39) missense probably damaging 1.00
R5724:Lct UTSW 1 128,228,073 (GRCm39) missense probably benign
R6026:Lct UTSW 1 128,227,755 (GRCm39) missense probably benign
R6044:Lct UTSW 1 128,235,717 (GRCm39) missense possibly damaging 0.95
R6175:Lct UTSW 1 128,255,451 (GRCm39) missense probably damaging 1.00
R6277:Lct UTSW 1 128,231,974 (GRCm39) missense probably benign 0.01
R6412:Lct UTSW 1 128,255,455 (GRCm39) missense probably benign 0.00
R6480:Lct UTSW 1 128,222,057 (GRCm39) missense probably damaging 1.00
R6526:Lct UTSW 1 128,228,215 (GRCm39) missense probably benign 0.05
R6620:Lct UTSW 1 128,222,809 (GRCm39) critical splice donor site probably null
R7214:Lct UTSW 1 128,228,197 (GRCm39) missense probably benign 0.00
R7308:Lct UTSW 1 128,246,824 (GRCm39) missense probably benign 0.00
R7577:Lct UTSW 1 128,228,469 (GRCm39) missense probably damaging 0.99
R7626:Lct UTSW 1 128,212,932 (GRCm39) missense probably damaging 1.00
R7737:Lct UTSW 1 128,226,430 (GRCm39) missense probably benign 0.12
R7901:Lct UTSW 1 128,216,722 (GRCm39) missense probably benign 0.44
R8033:Lct UTSW 1 128,212,996 (GRCm39) missense probably benign 0.03
R8373:Lct UTSW 1 128,231,577 (GRCm39) missense probably damaging 1.00
R8504:Lct UTSW 1 128,215,306 (GRCm39) missense probably damaging 1.00
R8751:Lct UTSW 1 128,221,534 (GRCm39) missense probably benign 0.18
R8781:Lct UTSW 1 128,215,261 (GRCm39) missense probably damaging 1.00
R8797:Lct UTSW 1 128,231,684 (GRCm39) missense possibly damaging 0.77
R8926:Lct UTSW 1 128,228,148 (GRCm39) missense probably damaging 1.00
R8949:Lct UTSW 1 128,221,929 (GRCm39) missense probably damaging 1.00
R8992:Lct UTSW 1 128,228,299 (GRCm39) missense probably damaging 1.00
R9138:Lct UTSW 1 128,227,894 (GRCm39) missense probably benign 0.03
R9260:Lct UTSW 1 128,227,704 (GRCm39) nonsense probably null
R9416:Lct UTSW 1 128,228,329 (GRCm39) missense possibly damaging 0.74
R9531:Lct UTSW 1 128,235,598 (GRCm39) missense probably benign 0.00
X0052:Lct UTSW 1 128,235,367 (GRCm39) missense probably damaging 1.00
YA93:Lct UTSW 1 128,229,057 (GRCm39) missense probably damaging 1.00
Z1176:Lct UTSW 1 128,215,348 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- AGTGTTGAGGCTCAGAGAGATGACC -3'
(R):5'- CAGCTATCATCAACTGGACGCTGAC -3'

Sequencing Primer
(F):5'- AGAGAGATGACCCCCTTCTG -3'
(R):5'- GAACTCTGAAGGTCAAGTCCTATCG -3'
Posted On 2013-05-23