Mutagenetix > Incidental Mutation

Incidental Mutation 'R5008:Lat2'

390278

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

042599-MU

Accession Numbers

Essential gene?

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

Stock #

R5008 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

134628876-134643879 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 134631991 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 152 (V152A)

Ref Sequence

ENSEMBL: ENSMUSP00000076824 (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

probably benign
Transcript: ENSMUST00000036362
AA Change: V164A

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000046900
Gene: ENSMUSG00000040751
AA Change: V164A

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 benign
Transcript: ENSMUST00000077636
AA Change: V152A

PolyPhen 2 Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000076824
Gene: ENSMUSG00000040751
AA Change: V152A

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

probably benign
Transcript: ENSMUST00000200998
AA Change: V164A

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000143977
Gene: ENSMUSG00000040751
AA Change: V164A

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201464

Predicted Effect

unknown
Transcript: ENSMUST00000201632
AA Change: V61A

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000202461

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000202746

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201832

Predicted Effect

probably benign
Transcript: ENSMUST00000202085

SMART Domains

Protein: ENSMUSP00000144611
Gene: ENSMUSG00000040751

Domain	Start	End	E-Value	Type
transmembrane domain	5	27	N/A	INTRINSIC
Pfam:LAT2	29	116	7.5e-29	PFAM

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 94.7%

Validation Efficiency

97% (73/75)

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: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310022A10Rik	C	G	7: 27,278,192 (GRCm39)	T242R	probably damaging	Het
2310057N15Rik	A	G	16: 88,570,663 (GRCm39)	Y126H	probably damaging	Het
Catsperg1	A	T	7: 28,894,859 (GRCm39)	Y579*	probably null	Het
Chchd5	A	T	2: 128,972,319 (GRCm39)		probably null	Het
Chd1l	T	C	3: 97,491,224 (GRCm39)	N423D	probably damaging	Het
Cntnap1	G	A	11: 101,079,567 (GRCm39)	W1268*	probably null	Het
Col2a1	G	A	15: 97,877,550 (GRCm39)	A1011V	probably benign	Het
Cst11	A	G	2: 148,612,325 (GRCm39)	I104T	probably benign	Het
Dctd	C	T	8: 48,590,449 (GRCm39)		probably benign	Het
Dnaaf4	T	C	9: 72,879,600 (GRCm39)		probably benign	Het
Dnah17	A	G	11: 118,001,403 (GRCm39)	F847L	probably benign	Het
Dspp	A	T	5: 104,323,439 (GRCm39)	H194L	possibly damaging	Het
Dync2i2	C	A	2: 29,922,781 (GRCm39)	R322L	probably benign	Het
Frmd5	C	A	2: 121,379,341 (GRCm39)	R414L	probably damaging	Het
Galnt3	C	A	2: 65,915,585 (GRCm39)	R592L	probably benign	Het
Gm38706	T	A	6: 130,461,580 (GRCm39)		noncoding transcript	Het
Gm38706	T	A	6: 130,461,983 (GRCm39)		noncoding transcript	Het
Hivep3	A	G	4: 119,956,114 (GRCm39)	K1477E	probably benign	Het
Igsf3	C	T	3: 101,358,233 (GRCm39)	T708M	probably damaging	Het
Ikzf4	T	G	10: 128,477,119 (GRCm39)	E64A	probably benign	Het
Klhl28	C	T	12: 65,004,001 (GRCm39)	E171K	probably damaging	Het
Krt87	T	A	15: 101,389,105 (GRCm39)	I76F	probably damaging	Het
Lrp12	C	T	15: 39,741,852 (GRCm39)	D288N	probably damaging	Het
Mdp1	C	T	14: 55,896,683 (GRCm39)	R126Q	probably damaging	Het
Msh2	C	A	17: 88,030,841 (GRCm39)	A906E	probably benign	Het
Muc6	G	A	7: 141,223,981 (GRCm39)		probably benign	Het
Myh4	T	A	11: 67,144,358 (GRCm39)	S1243T	probably benign	Het
Myo3b	T	A	2: 70,088,412 (GRCm39)	F892I	probably damaging	Het
Nckap5l	T	C	15: 99,323,731 (GRCm39)	N924S	possibly damaging	Het
Npnt	C	T	3: 132,612,218 (GRCm39)	C218Y	probably damaging	Het
Or2a20	T	A	6: 43,193,991 (GRCm39)	I48N	probably damaging	Het
Or2d2b	A	T	7: 106,705,288 (GRCm39)	M260K	probably damaging	Het
Or7a42	T	A	10: 78,791,905 (GRCm39)	F289I	probably damaging	Het
Pfkm	G	A	15: 98,020,570 (GRCm39)	C233Y	probably benign	Het
Pigq	A	G	17: 26,153,177 (GRCm39)	V338A	probably benign	Het
Pld4	A	T	12: 112,734,484 (GRCm39)	N415I	possibly damaging	Het
Pmm1	A	T	15: 81,842,095 (GRCm39)		probably null	Het
Polg	G	T	7: 79,109,822 (GRCm39)	P394T	probably damaging	Het
Polq	A	T	16: 36,882,749 (GRCm39)	I1359L	probably benign	Het
Pramel30	A	G	4: 144,057,836 (GRCm39)	S148G	probably benign	Het
Pros1	A	G	16: 62,748,548 (GRCm39)	N674D	possibly damaging	Het
Psme4	T	A	11: 30,806,896 (GRCm39)		probably benign	Het
Rasa3	A	T	8: 13,634,959 (GRCm39)	C453*	probably null	Het
Repin1	T	C	6: 48,573,542 (GRCm39)	V101A	probably damaging	Het
Rnf186	A	T	4: 138,694,540 (GRCm39)	M27L	probably benign	Het
Rpa1	A	G	11: 75,204,125 (GRCm39)		probably null	Het
Rph3a	G	T	5: 121,083,454 (GRCm39)	N605K	probably damaging	Het
Rps18	A	T	17: 34,171,258 (GRCm39)		probably null	Het
Scgn	A	G	13: 24,174,958 (GRCm39)	I20T	probably damaging	Het
Skint6	A	T	4: 112,848,452 (GRCm39)	V652E	possibly damaging	Het
Slc23a2	T	C	2: 131,943,414 (GRCm39)	H29R	probably damaging	Het
Slc34a3	C	T	2: 25,120,854 (GRCm39)	V383I	possibly damaging	Het
Slc5a1	A	G	5: 33,309,917 (GRCm39)	M382V	possibly damaging	Het
Slc5a3	T	A	16: 91,874,169 (GRCm39)	S75R	probably damaging	Het
Stat5b	G	C	11: 100,693,309 (GRCm39)	H111D	probably benign	Het
Tanc2	G	A	11: 105,515,886 (GRCm39)	M1I	probably null	Het
Tbcel	C	T	9: 42,327,419 (GRCm39)	G328E	probably damaging	Het
Tecta	C	A	9: 42,284,358 (GRCm39)	R909L	possibly damaging	Het
Tnip1	A	T	11: 54,828,810 (GRCm39)	M119K	probably benign	Het
Zbbx	A	C	3: 75,058,755 (GRCm39)	S51A	possibly damaging	Het
Zc3h12c	T	C	9: 52,028,000 (GRCm39)	N454S	probably benign	Het
Zfp980	G	A	4: 145,428,653 (GRCm39)	G461S	probably benign	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
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

Predicted Primers

PCR Primer
(F):5'- TTGGGTACAAGGAAGGCTCC -3'
(R):5'- GATTCTAAATCTCTGGTGCCTTTG -3'

Sequencing Primer
(F):5'- TCCACTGTGAAGTGAGCCAGAC -3'
(R):5'- TGCCTTTGGGTTAAGTTCACC -3'

Posted On

2016-06-06