Mutagenetix > Incidental Mutation

Incidental Mutation 'R0735:Lat2'

68224

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

038916-MU

Accession Numbers

Essential gene?

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

Stock #

R0735 (G1)

Quality Score

113

Status

Validated

Chromosome

Chromosomal Location

134628876-134643879 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 134635637 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 59 (Y59C)

Ref Sequence

ENSEMBL: ENSMUSP00000143977 (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 damaging
Transcript: ENSMUST00000036362
AA Change: Y59C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000046900
Gene: ENSMUSG00000040751
AA Change: Y59C

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: Y59C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000076824
Gene: ENSMUSG00000040751
AA Change: Y59C

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000200737
AA Change: Y59C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000143998
Gene: ENSMUSG00000040751
AA Change: Y59C

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 damaging
Transcript: ENSMUST00000200998
AA Change: Y59C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000143977
Gene: ENSMUSG00000040751
AA Change: Y59C

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: ENSMUST00000201632

Predicted Effect

probably damaging
Transcript: ENSMUST00000202085
AA Change: Y59C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000144611
Gene: ENSMUSG00000040751
AA Change: Y59C

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: ENSMUST00000201832

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000202461

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000202746

Meta Mutation Damage Score

0.6382

Coding Region Coverage

1x: 99.5%
3x: 98.7%
10x: 96.7%
20x: 91.8%

Validation Efficiency

95% (73/77)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actr8	T	A	14: 29,711,669 (GRCm39)	M405K	probably benign	Het
Adam10	G	A	9: 70,655,533 (GRCm39)	V334I	possibly damaging	Het
Adgra2	G	T	8: 27,607,346 (GRCm39)	G686C	probably damaging	Het
Akap11	A	T	14: 78,747,518 (GRCm39)	I1623N	probably damaging	Het
Astn1	A	T	1: 158,299,959 (GRCm39)	T100S	possibly damaging	Het
B3galt1	A	C	2: 67,948,923 (GRCm39)	I213L	possibly damaging	Het
B4galnt4	A	G	7: 140,644,236 (GRCm39)	K101E	probably benign	Het
Brd10	A	T	19: 29,695,038 (GRCm39)	I1552K	possibly damaging	Het
Camsap2	A	G	1: 136,220,626 (GRCm39)	S324P	probably damaging	Het
Chrnb4	A	G	9: 54,951,084 (GRCm39)	S60P	probably damaging	Het
Cpne1	A	G	2: 155,920,670 (GRCm39)		probably null	Het
Cubn	G	A	2: 13,496,500 (GRCm39)		probably benign	Het
Cul7	T	A	17: 46,974,116 (GRCm39)	L1467H	probably damaging	Het
Cxcl15	T	C	5: 90,949,153 (GRCm39)	M106T	probably benign	Het
Cyp2c23	A	T	19: 44,005,249 (GRCm39)	M140K	probably damaging	Het
Dgke	A	G	11: 88,950,901 (GRCm39)	F104S	probably benign	Het
Dhx36	T	A	3: 62,380,150 (GRCm39)	M849L	probably benign	Het
Dnah7a	C	T	1: 53,583,670 (GRCm39)	E1522K	possibly damaging	Het
Edil3	G	T	13: 89,325,297 (GRCm39)	V219F	probably damaging	Het
Egln1	A	G	8: 125,675,234 (GRCm39)	V187A	possibly damaging	Het
Fam193a	T	C	5: 34,596,722 (GRCm39)	I455T	possibly damaging	Het
Fdft1	A	T	14: 63,400,869 (GRCm39)	I88N	probably damaging	Het
Fem1c	G	A	18: 46,638,227 (GRCm39)	R592C	probably benign	Het
Frs2	T	A	10: 116,910,487 (GRCm39)	S292C	probably damaging	Het
Gpr107	T	A	2: 31,062,006 (GRCm39)	F145I	probably benign	Het
Gpr153	T	A	4: 152,363,830 (GRCm39)	C83*	probably null	Het
H2-Q7	T	G	17: 35,659,162 (GRCm39)		probably null	Het
Hsp90b1	A	T	10: 86,531,612 (GRCm39)		probably benign	Het
Kcnk1	C	A	8: 126,752,028 (GRCm39)	N211K	probably damaging	Het
Klb	T	C	5: 65,537,070 (GRCm39)	V800A	probably benign	Het
Mlkl	A	T	8: 112,054,433 (GRCm39)		probably benign	Het
Mroh2a	G	A	1: 88,171,672 (GRCm39)	R770Q	probably damaging	Het
Mtbp	T	A	15: 55,426,338 (GRCm39)	C93*	probably null	Het
Myo7a	A	G	7: 97,730,387 (GRCm39)		probably benign	Het
Myt1	G	A	2: 181,449,180 (GRCm39)		probably benign	Het
Ogfrl1	T	C	1: 23,414,835 (GRCm39)	Q224R	possibly damaging	Het
Or10j2	A	G	1: 173,098,569 (GRCm39)	T276A	probably benign	Het
Or56b2	A	T	7: 104,338,026 (GRCm39)	H268L	probably damaging	Het
Osbpl2	A	G	2: 179,792,083 (GRCm39)		probably benign	Het
Pira13	T	C	7: 3,824,781 (GRCm39)	T533A	possibly damaging	Het
Plb1	C	T	5: 32,442,264 (GRCm39)	T252M	possibly damaging	Het
Ptpro	T	A	6: 137,420,592 (GRCm39)	V1007D	probably damaging	Het
Rbsn	T	C	6: 92,166,674 (GRCm39)	T657A	probably benign	Het
Rims4	C	T	2: 163,705,849 (GRCm39)	V262M	possibly damaging	Het
Rps6kb2	C	A	19: 4,207,882 (GRCm39)	S348I	probably benign	Het
Rsrp1	C	T	4: 134,651,568 (GRCm39)	R111W	unknown	Het
Ryr3	T	C	2: 112,563,327 (GRCm39)	T2933A	probably benign	Het
Scara5	A	G	14: 65,968,468 (GRCm39)	D247G	possibly damaging	Het
Slc7a11	C	T	3: 50,378,545 (GRCm39)	S231N	probably benign	Het
Sod2	A	T	17: 13,229,451 (GRCm39)	N91Y	probably damaging	Het
Spesp1	A	T	9: 62,179,967 (GRCm39)	S314T	probably benign	Het
St3gal1	C	A	15: 66,985,536 (GRCm39)	M39I	probably benign	Het
Stat6	A	T	10: 127,494,110 (GRCm39)	I646F	probably damaging	Het
Tdrd1	A	T	19: 56,854,410 (GRCm39)	K1119*	probably null	Het
Thbs2	A	G	17: 14,900,077 (GRCm39)	I600T	probably benign	Het
Tor1a	A	G	2: 30,853,850 (GRCm39)	V160A	probably damaging	Het
Trdmt1	T	G	2: 13,528,249 (GRCm39)	D104A	probably benign	Het
Trim58	T	C	11: 58,542,219 (GRCm39)	V393A	probably benign	Het
Trip4	C	T	9: 65,792,200 (GRCm39)		probably benign	Het
Trip6	T	C	5: 137,309,083 (GRCm39)	E341G	probably benign	Het
Ttn	T	A	2: 76,545,539 (GRCm39)	I32595F	probably damaging	Het
Ubr4	T	A	4: 139,155,339 (GRCm39)		probably null	Het
Ush2a	G	A	1: 188,596,890 (GRCm39)	V3877I	probably benign	Het
Vmn1r29	G	T	6: 58,284,717 (GRCm39)	G146C	probably damaging	Het
Vmn2r53	A	G	7: 12,315,707 (GRCm39)	V704A	probably benign	Het
Vmn2r7	C	T	3: 64,623,788 (GRCm39)	M268I	probably benign	Het
Wnt7b	G	A	15: 85,421,696 (GRCm39)	T248M	probably damaging	Het
Xab2	G	A	8: 3,663,649 (GRCm39)	P394S	possibly damaging	Het
Zfp663	A	G	2: 165,200,995 (GRCm39)	V13A	probably damaging	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
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
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'- TCACTTACCCTCAAGGTGGGAGAAC -3'
(R):5'- ACAGACAGACACATTTCTATGCTCAGC -3'

Sequencing Primer
(F):5'- ACATAGTGAGGTCTAGCCCTG -3'
(R):5'- gacacatttctatgctcagctCTTC -3'

Posted On

2013-09-03