Mutagenetix > Incidental Mutation

Incidental Mutation 'R7512:Lat2'

582142

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

045585-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.050) question?

Stock #

R7512 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

134628876-134643879 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 134634798 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 114 (D114V)

Ref Sequence

ENSEMBL: ENSMUSP00000144611 (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

Domain	Start	End	E-Value	Type
AAA	63	189	9.42e-13	SMART
Pfam:Rep_fac_C	253	338	3.1e-19	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000036362
AA Change: D110V

PolyPhen 2 Score 0.864 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000046900
Gene: ENSMUSG00000040751
AA Change: D110V

Domain	Start	End	E-Value	Type
low complexity region	4	25	N/A	INTRINSIC
Pfam:LAT2	29	197	6.6e-82	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000077636
AA Change: D98V

PolyPhen 2 Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000076824
Gene: ENSMUSG00000040751
AA Change: D98V

Domain	Start	End	E-Value	Type
signal peptide	1	29	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000200737

SMART Domains

Protein: ENSMUSP00000143998
Gene: ENSMUSG00000040751

Domain	Start	End	E-Value	Type
transmembrane domain	5	27	N/A	INTRINSIC
Pfam:LAT2	29	114	9.5e-22	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000200945

Predicted Effect

possibly damaging
Transcript: ENSMUST00000200998
AA Change: D110V

PolyPhen 2 Score 0.864 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000143977
Gene: ENSMUSG00000040751
AA Change: D110V

Domain	Start	End	E-Value	Type
low complexity region	4	25	N/A	INTRINSIC
Pfam:LAT2	29	197	6.6e-82	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000202085
AA Change: D114V

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000144611
Gene: ENSMUSG00000040751
AA Change: D114V

Domain	Start	End	E-Value	Type
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: ENSMUST00000201832

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000202746

Coding Region Coverage

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

Validation Efficiency

100% (59/59)

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8b	C	T	11: 109,829,275 (GRCm39)	A1395T	probably benign	Het
Ank3	A	G	10: 69,826,691 (GRCm39)	K1787E		Het
Atg2a	C	T	19: 6,310,106 (GRCm39)	A1763V	probably damaging	Het
Bdp1	T	C	13: 100,187,457 (GRCm39)	I1637V	probably benign	Het
C1ra	G	A	6: 124,494,684 (GRCm39)	E316K	probably benign	Het
Camsap3	A	G	8: 3,648,740 (GRCm39)	T20A	probably benign	Het
Ccnt2	T	A	1: 127,730,031 (GRCm39)	S303T	possibly damaging	Het
Cdh3	C	T	8: 107,265,640 (GRCm39)	Q228*	probably null	Het
Col19a1	C	T	1: 24,356,788 (GRCm39)	G632R	probably damaging	Het
Dock2	A	C	11: 34,262,542 (GRCm39)	C938G	possibly damaging	Het
Dync1i1	G	T	6: 5,969,410 (GRCm39)	V412L	possibly damaging	Het
Eif1ad6	G	T	12: 87,668,751 (GRCm39)	E128*	probably null	Het
Entrep2	C	T	7: 64,805,918 (GRCm39)	A52T	probably benign	Het
Fam185a	G	A	5: 21,652,356 (GRCm39)		probably null	Het
Fcho1	A	G	8: 72,169,507 (GRCm39)	L133P	possibly damaging	Het
Galnt12	G	A	4: 47,108,406 (GRCm39)	R181H	possibly damaging	Het
Gen1	A	G	12: 11,310,977 (GRCm39)	V85A	possibly damaging	Het
Gm12185	A	T	11: 48,806,717 (GRCm39)	I158K	probably benign	Het
Gm5624	T	C	14: 44,799,312 (GRCm39)	R82G		Het
Grap2	A	C	15: 80,532,754 (GRCm39)	N307T	probably benign	Het
H6pd	A	G	4: 150,080,405 (GRCm39)	F147L	probably benign	Het
Haspin	A	T	11: 73,027,418 (GRCm39)	I557N	probably damaging	Het
Hectd4	A	T	5: 121,435,172 (GRCm39)	K961N	possibly damaging	Het
Helz2	A	G	2: 180,872,647 (GRCm39)	M2495T	probably benign	Het
Helz2	A	T	2: 180,877,393 (GRCm39)		probably null	Het
Impdh1	T	C	6: 29,207,168 (GRCm39)	I59V	probably benign	Het
Kcnn1	A	T	8: 71,307,293 (GRCm39)	L200Q	possibly damaging	Het
Kif5c	T	A	2: 49,590,977 (GRCm39)	H276Q	probably damaging	Het
Kntc1	T	C	5: 123,929,001 (GRCm39)	L1259P	probably damaging	Het
Krtap4-1	A	T	11: 99,518,859 (GRCm39)	C50*	probably null	Het
Lrrc41	A	G	4: 115,950,191 (GRCm39)	T535A	possibly damaging	Het
Ly75	A	T	2: 60,164,907 (GRCm39)	V757D	probably damaging	Het
Masp1	C	A	16: 23,288,874 (GRCm39)	R642L	probably damaging	Het
Morn3	A	G	5: 123,175,343 (GRCm39)		probably null	Het
Mpl	A	T	4: 118,306,089 (GRCm39)	I384N		Het
Mtmr14	C	T	6: 113,245,652 (GRCm39)	Q409*	probably null	Het
Nek1	T	A	8: 61,583,179 (GRCm39)	D1272E	probably benign	Het
Oit3	T	C	10: 59,274,716 (GRCm39)	Y28C	probably damaging	Het
Or2z8	T	A	8: 72,812,367 (GRCm39)	I281N	probably damaging	Het
Or4x12-ps1	A	G	2: 89,916,040 (GRCm39)	I255T	possibly damaging	Het
Or5ac22	T	A	16: 59,135,390 (GRCm39)	N127Y	probably damaging	Het
Pcdh15	T	C	10: 74,477,214 (GRCm39)	Y186H	possibly damaging	Het
Pcdhgb1	T	A	18: 37,815,418 (GRCm39)	D636E	probably damaging	Het
Pdgfra	A	T	5: 75,355,675 (GRCm39)	R1062*	probably null	Het
Pds5b	T	C	5: 150,711,807 (GRCm39)	F922L	probably damaging	Het
Pip5k1c	G	A	10: 81,150,953 (GRCm39)		probably null	Het
Ppp2r3d	T	C	9: 101,052,532 (GRCm39)	T226A	possibly damaging	Het
Ptprh	G	A	7: 4,574,780 (GRCm39)	T413I	possibly damaging	Het
Rora	C	A	9: 69,281,367 (GRCm39)	D382E	probably benign	Het
Sacs	T	A	14: 61,441,879 (GRCm39)	N1308K	probably benign	Het
Sgce	C	T	6: 4,707,192 (GRCm39)	D218N	possibly damaging	Het
Slc34a3	A	T	2: 25,122,253 (GRCm39)		probably null	Het
Slit1	T	C	19: 41,589,074 (GRCm39)	Y1471C	probably damaging	Het
Smarca2	G	T	19: 26,661,209 (GRCm39)	V935L	possibly damaging	Het
Smchd1	T	C	17: 71,688,364 (GRCm39)	N1298S	possibly damaging	Het
Sort1	T	A	3: 108,233,323 (GRCm39)		probably null	Het
Spata13	T	C	14: 60,989,226 (GRCm39)	L964P	probably damaging	Het
Spata31h1	G	A	10: 82,128,469 (GRCm39)	L1514F	probably benign	Het
Trav7-6	C	A	14: 53,954,552 (GRCm39)	D47E	probably benign	Het
Ubap2l	A	G	3: 89,917,803 (GRCm39)	F864L	unknown	Het
Vmn2r102	C	T	17: 19,914,363 (GRCm39)	P643S	probably damaging	Het
Zfp112	T	A	7: 23,824,604 (GRCm39)	C195S	possibly damaging	Het
Zfp764l1	C	T	7: 126,992,496 (GRCm39)	C38Y	probably null	Het

Other mutations in Lat2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
R8811:Lat2	UTSW	5	134,635,553 (GRCm39)	intron	probably benign

Predicted Primers

PCR Primer
(F):5'- TCTCCAAATGGCCAGGATGG -3'
(R):5'- CAAAGGTCTGGCCATTCAAAGC -3'

Sequencing Primer
(F):5'- CCAGGATGGGTGGCTACC -3'
(R):5'- TCTAGCCTAGCCTAGCCTAGCAG -3'

Posted On

2019-10-17