Mutagenetix > Incidental Mutation

Incidental Mutation 'R9416:Lct'

712029

Institutional Source

Beutler Lab

Gene Symbol

Lct

Ensembl Gene

ENSMUSG00000026354

Gene Name

lactase

Synonyms

LPH, LOC226413, Lphl

MMRRC Submission

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9416 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

128212493-128256055 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 128228329 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 1055 (T1055A)

Ref Sequence

ENSEMBL: ENSMUSP00000073190 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000073490]

AlphaFold

F8VPT3

Predicted Effect

possibly damaging
Transcript: ENSMUST00000073490
AA Change: T1055A

PolyPhen 2 Score 0.742 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000073190
Gene: ENSMUSG00000026354
AA Change: T1055A

Domain	Start	End	E-Value	Type
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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

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: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamtsl1	C	T	4: 86,342,477 (GRCm39)	T1672I	probably damaging	Het
Ahnak	T	G	19: 8,990,266 (GRCm39)	M3850R	unknown	Het
Cacna1s	T	A	1: 136,022,689 (GRCm39)	L874Q	possibly damaging	Het
Cacna2d4	A	T	6: 119,274,479 (GRCm39)	D622V	probably benign	Het
Ccdc150	T	C	1: 54,317,990 (GRCm39)	S310P	probably damaging	Het
Cecr2	A	T	6: 120,735,538 (GRCm39)	N148Y		Het
Celsr2	T	C	3: 108,322,084 (GRCm39)	T243A	probably damaging	Het
Coro1b	C	T	19: 4,201,473 (GRCm39)	T279I	probably damaging	Het
Cyp51	A	G	5: 4,150,198 (GRCm39)	I175T	probably damaging	Het
Dnajc21	T	C	15: 10,462,048 (GRCm39)	I118V	possibly damaging	Het
Dtna	T	C	18: 23,780,112 (GRCm39)		probably null	Het
Etl4	A	G	2: 20,748,784 (GRCm39)	K374R	probably benign	Het
Fance	G	A	17: 28,537,327 (GRCm39)	C53Y	probably damaging	Het
Gm14496	G	T	2: 181,640,647 (GRCm39)	C538F	probably damaging	Het
Gon4l	T	A	3: 88,803,538 (GRCm39)	V1383D	probably benign	Het
Gpr6	C	A	10: 40,946,944 (GRCm39)	D213Y	possibly damaging	Het
Has2	A	G	15: 56,531,684 (GRCm39)	Y344H	probably damaging	Het
Kcnh2	A	T	5: 24,537,964 (GRCm39)	M133K	probably benign	Het
Kdm5a	A	G	6: 120,365,056 (GRCm39)	H152R	probably damaging	Het
Klhl33	C	T	14: 51,130,225 (GRCm39)	R163H	probably damaging	Het
Lax1	T	A	1: 133,611,752 (GRCm39)	Q61L	probably benign	Het
Lrrc8c	A	G	5: 105,756,163 (GRCm39)	Y646C	possibly damaging	Het
Mtarc1	T	C	1: 184,527,633 (GRCm39)	T274A	probably benign	Het
Myo1b	A	G	1: 51,902,577 (GRCm39)	V51A	probably damaging	Het
Naip2	T	A	13: 100,298,243 (GRCm39)	S598C	probably damaging	Het
Neb	A	G	2: 52,137,215 (GRCm39)	S250P		Het
Nim1k	A	T	13: 120,189,362 (GRCm39)	C16S	probably benign	Het
Oosp1	T	C	19: 11,664,769 (GRCm39)	T96A	probably damaging	Het
Or1e1c	T	C	11: 73,265,790 (GRCm39)	S75P	probably damaging	Het
Or2q1	G	T	6: 42,795,197 (GRCm39)	R264L	probably benign	Het
Or8k17	T	A	2: 86,066,744 (GRCm39)	Q138L	probably damaging	Het
Pik3c2b	C	T	1: 133,005,187 (GRCm39)	R563C	probably damaging	Het
Ppp1r18	CGAGGAGGAGGAGGAGGAGGAGGA	CGAGGAGGAGGAGGAGGAGGA	17: 36,184,743 (GRCm39)		probably benign	Het
Prps1l1	T	A	12: 35,035,089 (GRCm39)	M68K		Het
Prr11	A	T	11: 86,992,254 (GRCm39)	L207*	probably null	Het
Psme3	T	C	11: 101,211,559 (GRCm39)	Y202H	probably damaging	Het
Ptma	A	G	1: 86,455,694 (GRCm39)	S57G	unknown	Het
Rab24	A	G	13: 55,468,049 (GRCm39)	V33A	unknown	Het
Reep6	A	G	10: 80,166,091 (GRCm39)	T83A	probably benign	Het
Semp2l2b	C	T	10: 21,943,752 (GRCm39)	R76Q	probably benign	Het
Shroom4	GCAACAACAACAACAACAACAACAACA	GCAACAACAACAACAACAACAACA	X: 6,536,131 (GRCm39)		probably benign	Het
Siglec1	T	C	2: 130,925,390 (GRCm39)	K357R	probably benign	Het
Slc2a4	T	A	11: 69,836,728 (GRCm39)	H167L	probably benign	Het
Slc8a3	T	A	12: 81,361,838 (GRCm39)	H327L	probably benign	Het
Slf1	G	A	13: 77,194,656 (GRCm39)	L890F		Het
Smchd1	A	C	17: 71,701,791 (GRCm39)	I1067R	probably benign	Het
Stk33	T	A	7: 108,940,689 (GRCm39)	N7I	probably benign	Het
Tex47	T	C	5: 7,355,194 (GRCm39)	M125T	possibly damaging	Het
Thada	A	T	17: 84,766,292 (GRCm39)	L38*	probably null	Het
Thbs1	A	G	2: 117,947,983 (GRCm39)	D381G	probably benign	Het
Uggt1	A	T	1: 36,203,603 (GRCm39)	V1009D		Het
Usp17la	A	T	7: 104,508,531 (GRCm39)		probably benign	Het
Zfp438	A	T	18: 5,214,054 (GRCm39)	N301K	probably benign	Het
Zfp606	T	A	7: 12,227,907 (GRCm39)	I676N	possibly damaging	Het

Other mutations in Lct

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
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'- GTTGAGGCTCAGAGAGATGACC -3'
(R):5'- CCTCGAATTTTCCCAACGGG -3'

Sequencing Primer
(F):5'- TCAGAGAGATGACCCCCTTCTG -3'
(R):5'- ACGGGAAGAAACAGTTCCATC -3'

Posted On

2022-05-16