Mutagenetix > Incidental Mutation

Incidental Mutation 'R2215:Lat'

241093

Institutional Source

Beutler Lab

Gene Symbol

Lat

Ensembl Gene

ENSMUSG00000030742

Gene Name

linker for activation of T cells

Synonyms

MMRRC Submission

040217-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.059) question?

Stock #

R2215 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

125962996-125968742 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 125967137 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glutamic Acid at position 139 (V139E)

Ref Sequence

ENSEMBL: ENSMUSP00000032997 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000032994] [ENSMUST00000032997] [ENSMUST00000119754] [ENSMUST00000119846] [ENSMUST00000138141] [ENSMUST00000206793] [ENSMUST00000205366] [ENSMUST00000205642] [ENSMUST00000205930] [ENSMUST00000150476]

AlphaFold

O54957

Predicted Effect

probably benign
Transcript: ENSMUST00000032994

SMART Domains

Protein: ENSMUSP00000032994
Gene: ENSMUSG00000030741

Domain	Start	End	E-Value	Type
low complexity region	14	34	N/A	INTRINSIC
Pfam:Sugar_tr	60	250	4.6e-15	PFAM
Pfam:OATP	60	385	1.5e-9	PFAM
Pfam:MFS_1	65	435	1.8e-34	PFAM
transmembrane domain	462	484	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000032997
AA Change: V139E

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

SMART Domains

Protein: ENSMUSP00000032997
Gene: ENSMUSG00000030742
AA Change: V139E

Domain	Start	End	E-Value	Type
Pfam:LAT	1	242	4.3e-121	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000119754

SMART Domains

Protein: ENSMUSP00000112555
Gene: ENSMUSG00000030741

Domain	Start	End	E-Value	Type
low complexity region	14	34	N/A	INTRINSIC
Pfam:OATP	58	147	1.2e-8	PFAM
Pfam:Sugar_tr	60	250	1.3e-14	PFAM
Pfam:MFS_1	65	430	2.4e-34	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000119846

SMART Domains

Protein: ENSMUSP00000112954
Gene: ENSMUSG00000030741

Domain	Start	End	E-Value	Type
low complexity region	14	34	N/A	INTRINSIC
Pfam:OATP	58	147	1.4e-8	PFAM
Pfam:Sugar_tr	60	250	1.5e-14	PFAM
Pfam:MFS_1	65	433	2.5e-26	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126810

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137263

Predicted Effect

probably benign
Transcript: ENSMUST00000138141

SMART Domains

Protein: ENSMUSP00000117803
Gene: ENSMUSG00000030741

Domain	Start	End	E-Value	Type
low complexity region	14	34	N/A	INTRINSIC
Pfam:OATP	58	151	1.4e-9	PFAM
Pfam:MFS_1	65	149	1.5e-11	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000206793
AA Change: V129E

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

Predicted Effect

probably benign
Transcript: ENSMUST00000205366

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206731

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152000

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205398

Predicted Effect

probably benign
Transcript: ENSMUST00000205642

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184637

Predicted Effect

probably benign
Transcript: ENSMUST00000205930

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205426

Predicted Effect

probably benign
Transcript: ENSMUST00000150476

SMART Domains

Protein: ENSMUSP00000115152
Gene: ENSMUSG00000030741

Domain	Start	End	E-Value	Type
Pfam:OATP	28	120	1.3e-8	PFAM
Pfam:Sugar_tr	28	220	1.6e-15	PFAM
Pfam:MFS_1	35	237	2.4e-31	PFAM

Meta Mutation Damage Score

0.4398

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.3%

Validation Efficiency

100% (68/68)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is phosphorylated by ZAP-70/Syk protein tyrosine kinases following activation of the T-cell antigen receptor (TCR) signal transduction pathway. This transmembrane protein localizes to lipid rafts and acts as a docking site for SH2 domain-containing proteins. Upon phosphorylation, this protein recruits multiple adaptor proteins and downstream signaling molecules into multimolecular signaling complexes located near the site of TCR engagement. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations exhibit blockage of intra-thymic lymphocyte development at the double negative stage and absence of mature peripheral T cells. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acaca	T	A	11: 84,254,619 (GRCm39)	S1899T	probably damaging	Het
Accs	G	T	2: 93,672,243 (GRCm39)	N208K	probably benign	Het
Actn4	C	A	7: 28,618,178 (GRCm39)	V22L	possibly damaging	Het
Adam21	A	G	12: 81,607,064 (GRCm39)	S233P	probably damaging	Het
Adrm1b	G	A	3: 92,335,730 (GRCm39)	A324V	probably damaging	Het
Agmat	C	T	4: 141,476,899 (GRCm39)	R102C	probably benign	Het
Akap8l	T	C	17: 32,540,569 (GRCm39)	E608G	possibly damaging	Het
Arap2	T	C	5: 62,834,519 (GRCm39)	I788V	probably damaging	Het
Arhgef12	G	T	9: 42,917,167 (GRCm39)	H391N	probably damaging	Het
Arhgef28	G	T	13: 98,187,529 (GRCm39)	H255Q	possibly damaging	Het
Baz1a	G	A	12: 55,022,154 (GRCm39)	R43*	probably null	Het
Bcas3	T	C	11: 85,692,769 (GRCm39)	S862P	probably damaging	Het
Blm	A	T	7: 80,149,595 (GRCm39)	H671Q	possibly damaging	Het
Bmp8a	C	T	4: 123,218,911 (GRCm39)	V166I	probably benign	Het
Cep120	G	T	18: 53,860,707 (GRCm39)	P241Q	probably damaging	Het
Col14a1	G	A	15: 55,244,238 (GRCm39)	G437E	unknown	Het
Cyp2a5	T	C	7: 26,539,900 (GRCm39)	L3S	probably damaging	Het
D16Ertd472e	T	C	16: 78,342,155 (GRCm39)	T242A	probably benign	Het
Dach1	A	G	14: 98,405,917 (GRCm39)		probably null	Het
Ddx20	A	T	3: 105,587,656 (GRCm39)		probably benign	Het
Eif4enif1	A	G	11: 3,177,476 (GRCm39)	S185G	probably damaging	Het
Ep400	A	T	5: 110,841,421 (GRCm39)		probably benign	Het
Fam117b	T	A	1: 60,008,219 (GRCm39)	I351K	probably damaging	Het
Fbxo31	T	C	8: 122,293,050 (GRCm39)	I112V	probably benign	Het
Galntl5	A	T	5: 25,403,476 (GRCm39)	N149I	probably damaging	Het
Gja8	A	T	3: 96,827,218 (GRCm39)	F148Y	probably damaging	Het
Gpatch1	A	T	7: 34,993,252 (GRCm39)	L531Q	possibly damaging	Het
Gprin1	G	A	13: 54,888,046 (GRCm39)	T76M	probably damaging	Het
Htr4	T	A	18: 62,546,787 (GRCm39)	C113*	probably null	Het
Igf1r	T	A	7: 67,814,982 (GRCm39)	D294E	probably benign	Het
Kdm6b	G	A	11: 69,295,870 (GRCm39)	P799L	unknown	Het
Lrrc34	G	A	3: 30,697,678 (GRCm39)	R51C	probably benign	Het
Map3k1	A	G	13: 111,892,322 (GRCm39)	S978P	probably benign	Het
Masp1	T	A	16: 23,271,271 (GRCm39)	D659V	possibly damaging	Het
Mcam	A	T	9: 44,051,250 (GRCm39)	R415*	probably null	Het
Mtmr10	A	G	7: 63,987,403 (GRCm39)	T648A	probably benign	Het
Myh2	T	C	11: 67,082,563 (GRCm39)	W1378R	probably benign	Het
Nipsnap2	A	G	5: 129,816,649 (GRCm39)	E64G	probably damaging	Het
Or4a68	T	C	2: 89,270,381 (GRCm39)	M81V	probably benign	Het
Or52n4b	T	C	7: 108,144,095 (GRCm39)	L119P	probably damaging	Het
Or6c3	A	T	10: 129,309,289 (GRCm39)	I243F	probably damaging	Het
Or9s27	G	A	1: 92,516,708 (GRCm39)	V219I	probably benign	Het
Pcdhb8	T	G	18: 37,490,127 (GRCm39)	S602A	probably damaging	Het
Peg10	A	T	6: 4,756,918 (GRCm39)		probably benign	Het
Pld1	A	T	3: 28,132,542 (GRCm39)	I577F	probably benign	Het
Plekhm1	A	T	11: 103,267,811 (GRCm39)	I720N	probably damaging	Het
Ppp2r1a	A	G	17: 21,182,005 (GRCm39)		probably null	Het
Retreg3	G	T	11: 101,010,459 (GRCm39)	Y49*	probably null	Het
Rrp36	T	C	17: 46,983,746 (GRCm39)	E22G	possibly damaging	Het
Sec14l2	C	A	11: 4,059,169 (GRCm39)	A167S	probably damaging	Het
Sema5b	A	G	16: 35,480,585 (GRCm39)	T751A	probably damaging	Het
Smarcc1	C	A	9: 110,066,907 (GRCm39)		probably benign	Het
Smox	T	C	2: 131,362,190 (GRCm39)		probably null	Het
Spats2l	A	T	1: 57,985,575 (GRCm39)	T543S	possibly damaging	Het
Sppl2a	G	T	2: 126,769,754 (GRCm39)	T34K	probably benign	Het
Svep1	T	C	4: 58,138,602 (GRCm39)		probably benign	Het
Tet2	T	A	3: 133,192,362 (GRCm39)	I691F	probably benign	Het
Tnxb	T	C	17: 34,923,114 (GRCm39)	Y2566H	possibly damaging	Het
Ttn	T	C	2: 76,570,853 (GRCm39)	E26680G	probably damaging	Het
Txlna	T	C	4: 129,533,111 (GRCm39)	E139G	possibly damaging	Het
Ubap2	T	C	4: 41,196,483 (GRCm39)		probably null	Het
Ubr3	A	T	2: 69,809,661 (GRCm39)		probably null	Het
Usp37	A	C	1: 74,483,685 (GRCm39)	F844V	probably damaging	Het
Usp6nl	A	G	2: 6,429,150 (GRCm39)	D204G	probably damaging	Het
Vmn1r230	T	C	17: 21,067,684 (GRCm39)	I291T	probably benign	Het
Zfp229	T	G	17: 21,965,258 (GRCm39)	V496G	possibly damaging	Het

Other mutations in Lat

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01775:Lat	APN	7	125,967,261 (GRCm39)	missense	probably benign	0.05
R4947:Lat	UTSW	7	125,967,110 (GRCm39)	missense	probably benign	0.03
R7058:Lat	UTSW	7	125,968,318 (GRCm39)	critical splice donor site	probably null
R7705:Lat	UTSW	7	125,963,612 (GRCm39)	missense	probably damaging	1.00
X0025:Lat	UTSW	7	125,963,463 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- CCAACGTCTACAGGAGGAAATG -3'
(R):5'- TGGCAAGCTACGAGAACCAG -3'

Sequencing Primer
(F):5'- AAGGGCGGCAATCGTCAC -3'
(R):5'- CAAGCTACGAGAACCAGGGTGG -3'

Posted On

2014-10-15