Incidental Mutation 'R0755:Lct'
ID 70381
Institutional Source Beutler Lab
Gene Symbol Lct
Ensembl Gene ENSMUSG00000026354
Gene Name lactase
Synonyms LPH, LOC226413, Lphl
MMRRC Submission 038935-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0755 (G1)
Quality Score 225
Status Not validated
Chromosome 1
Chromosomal Location 128212493-128256055 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 128221872 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 1556 (S1556T)
Ref Sequence ENSEMBL: ENSMUSP00000073190 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000073490]
AlphaFold F8VPT3
Predicted Effect possibly damaging
Transcript: ENSMUST00000073490
AA Change: S1556T

PolyPhen 2 Score 0.458 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000073190
Gene: ENSMUSG00000026354
AA Change: S1556T

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000162067
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 93.8%
Validation Efficiency
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: 94 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A730061H03Rik A T 14: 55,797,638 (GRCm39) probably benign Het
Acin1 A G 14: 54,889,292 (GRCm39) M1T probably null Het
Akp3 G A 1: 87,055,593 (GRCm39) G547R unknown Het
Aldh1a1 A G 19: 20,595,358 (GRCm39) M96V probably benign Het
Ankfn1 T A 11: 89,282,913 (GRCm39) M245L probably benign Het
Arhgap19 T C 19: 41,769,614 (GRCm39) K54E probably damaging Het
Atp1a2 T C 1: 172,116,948 (GRCm39) Q223R probably benign Het
Atp8a2 C T 14: 60,247,330 (GRCm39) V557I possibly damaging Het
AU041133 A T 10: 81,986,724 (GRCm39) K126* probably null Het
Axin1 T A 17: 26,401,480 (GRCm39) Y351N possibly damaging Het
Baiap2l1 T C 5: 144,221,367 (GRCm39) K176E probably damaging Het
Baz2a C T 10: 127,955,560 (GRCm39) T848I possibly damaging Het
Bbs2 A C 8: 94,808,708 (GRCm39) V333G probably benign Het
BC051019 G A 7: 109,315,302 (GRCm39) Q318* probably null Het
Bltp1 T C 3: 37,000,513 (GRCm39) S1231P probably damaging Het
Cdc37 C T 9: 21,051,160 (GRCm39) D362N probably damaging Het
Cep170 A T 1: 176,583,319 (GRCm39) V1020E probably damaging Het
Chrm4 T C 2: 91,758,747 (GRCm39) V385A probably benign Het
Cntrl G A 2: 35,035,151 (GRCm39) S373N probably damaging Het
Col23a1 G A 11: 51,467,706 (GRCm39) G19D probably damaging Het
Cyb5r4 G T 9: 86,911,625 (GRCm39) A100S probably damaging Het
Dctn1 C T 6: 83,166,059 (GRCm39) P115S probably damaging Het
Dhrs2 C T 14: 55,472,247 (GRCm39) T46M probably damaging Het
Disp2 T C 2: 118,620,243 (GRCm39) F325S probably benign Het
Dnah11 T G 12: 117,918,564 (GRCm39) T3456P possibly damaging Het
Dnah11 C A 12: 118,162,360 (GRCm39) V70F probably benign Het
Duoxa1 T A 2: 122,135,161 (GRCm39) T195S probably benign Het
Dync2i1 T C 12: 116,175,412 (GRCm39) I922V probably benign Het
Eif2ak1 T A 5: 143,821,742 (GRCm39) F353I possibly damaging Het
Esam A G 9: 37,447,998 (GRCm39) T211A probably damaging Het
Faf1 A G 4: 109,819,036 (GRCm39) N636S probably benign Het
Fbxo25 A G 8: 13,985,219 (GRCm39) Y305C probably benign Het
Fchsd1 C T 18: 38,101,803 (GRCm39) probably null Het
Fdxacb1 T A 9: 50,683,025 (GRCm39) D329E possibly damaging Het
Gvin2 A T 7: 105,545,892 (GRCm39) F2387I possibly damaging Het
Hbq1b A T 11: 32,237,104 (GRCm39) probably null Het
Hmcn2 T A 2: 31,343,172 (GRCm39) V4566E probably damaging Het
Igkv6-29 G A 6: 70,116,053 (GRCm39) T5I probably benign Het
Itfg1 A T 8: 86,452,834 (GRCm39) D511E possibly damaging Het
Jmjd1c C T 10: 66,932,378 (GRCm39) probably benign Het
Kat6b T A 14: 21,687,661 (GRCm39) M570K probably damaging Het
Kdm4d T A 9: 14,375,591 (GRCm39) K89M probably damaging Het
Krt19 A T 11: 100,032,965 (GRCm39) D194E possibly damaging Het
Lamc1 A T 1: 153,123,196 (GRCm39) Y665N possibly damaging Het
Macf1 A G 4: 123,263,719 (GRCm39) L4924P probably damaging Het
Mef2c G A 13: 83,804,472 (GRCm39) probably null Het
Mff G A 1: 82,728,326 (GRCm39) probably null Het
Mycbp2 A T 14: 103,412,230 (GRCm39) L2581Q probably damaging Het
Mylk G C 16: 34,699,845 (GRCm39) E403Q possibly damaging Het
Nos3 T A 5: 24,572,295 (GRCm39) L123M probably damaging Het
Ntn5 C T 7: 45,335,952 (GRCm39) P128S probably benign Het
Nudt9 T C 5: 104,212,920 (GRCm39) V331A probably damaging Het
Or2y3 A T 17: 38,393,085 (GRCm39) Y261* probably null Het
Or7g34 T C 9: 19,478,415 (GRCm39) I88M possibly damaging Het
Pcdh7 A T 5: 57,877,664 (GRCm39) K406N possibly damaging Het
Pkdrej T A 15: 85,700,336 (GRCm39) I1867L probably benign Het
Plppr4 C T 3: 117,116,319 (GRCm39) G455R possibly damaging Het
Pramel11 A G 4: 143,624,299 (GRCm39) V66A probably damaging Het
Prkag2 G C 5: 25,152,629 (GRCm39) S158R probably benign Het
Ptprq T G 10: 107,418,400 (GRCm39) T1659P probably benign Het
Rasl12 A G 9: 65,318,241 (GRCm39) K202E probably benign Het
Rb1 A C 14: 73,434,653 (GRCm39) *922G probably null Het
Rsf1 C T 7: 97,229,174 (GRCm39) P22S probably damaging Het
Scn1a T G 2: 66,151,379 (GRCm39) T797P probably damaging Het
Sgsm2 A G 11: 74,756,323 (GRCm39) V342A probably damaging Het
Slc22a7 T G 17: 46,749,113 (GRCm39) H68P possibly damaging Het
Slc4a2 G A 5: 24,640,575 (GRCm39) A652T probably benign Het
Slc5a1 T A 5: 33,290,733 (GRCm39) L106M probably benign Het
Slco1c1 C T 6: 141,477,258 (GRCm39) P19S probably damaging Het
Snx1 A G 9: 66,005,738 (GRCm39) F127S probably damaging Het
Snx31 A T 15: 36,534,576 (GRCm39) I199N probably damaging Het
Snx33 T C 9: 56,832,741 (GRCm39) I443V possibly damaging Het
Sptbn1 A G 11: 30,089,016 (GRCm39) F749L probably damaging Het
Stoml3 T A 3: 53,405,559 (GRCm39) Y53* probably null Het
Stxbp2 A G 8: 3,692,019 (GRCm39) T554A probably benign Het
Tal1 T C 4: 114,925,573 (GRCm39) I214T probably damaging Het
Tas2r140 T A 6: 40,468,344 (GRCm39) I58N probably damaging Het
Thap1 A G 8: 26,648,501 (GRCm39) Y8C probably damaging Het
Thsd7a A T 6: 12,555,368 (GRCm39) L172Q probably damaging Het
Ube3c T A 5: 29,842,740 (GRCm39) D735E probably damaging Het
Unc80 G A 1: 66,544,082 (GRCm39) D402N probably damaging Het
Upf1 G T 8: 70,786,779 (GRCm39) R902S probably benign Het
Urb1 A G 16: 90,570,982 (GRCm39) Y1276H probably damaging Het
Urb1 A T 16: 90,576,026 (GRCm39) F843L probably benign Het
Vmn1r198 C T 13: 22,539,402 (GRCm39) T296I probably benign Het
Vmn1r33 A T 6: 66,588,892 (GRCm39) S221T probably damaging Het
Vmn2r103 A G 17: 19,993,830 (GRCm39) D69G probably benign Het
Vmn2r14 T G 5: 109,364,226 (GRCm39) L563F possibly damaging Het
Vmn2r60 G A 7: 41,844,869 (GRCm39) G744D probably damaging Het
Vstm4 T C 14: 32,614,601 (GRCm39) V181A probably damaging Het
Wdr72 G A 9: 74,052,376 (GRCm39) V136I probably benign Het
Zfp236 T A 18: 82,638,457 (GRCm39) N1388Y probably damaging Het
Zfp53 T A 17: 21,728,839 (GRCm39) F291I probably damaging Het
Zfp944 A T 17: 22,558,889 (GRCm39) H119Q possibly 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
R0492:Lct UTSW 1 128,228,319 (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
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'- CGGATGGAATGGAGGATTTGACCC -3'
(R):5'- CGCTCTGACTTGCTCATAGGTGAC -3'

Sequencing Primer
(F):5'- GAAGACCCGGATTCCAGTTTC -3'
(R):5'- CTCATAGGTGACCATGTATCACTGG -3'
Posted On 2013-09-30