Mutagenetix > Incidental Mutation

Incidental Mutation 'R7058:Lat'

548066

Institutional Source

Beutler Lab

Gene Symbol

Lat

Ensembl Gene

ENSMUSG00000030742

Gene Name

linker for activation of T cells

Synonyms

MMRRC Submission

045155-MU

Accession Numbers

Essential gene?

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

Stock #

R7058 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

125962996-125968742 bp(-) (GRCm39)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

A to G at 125968318 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000145773 (fasta)

Gene Model

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

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 null
Transcript: ENSMUST00000032997

SMART Domains

Protein: ENSMUSP00000032997
Gene: ENSMUSG00000030742

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

Predicted Effect

probably null
Transcript: ENSMUST00000032997

SMART Domains

Protein: ENSMUSP00000032997
Gene: ENSMUSG00000030742

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

Predicted Effect

probably null
Transcript: ENSMUST00000032997

SMART Domains

Protein: ENSMUSP00000032997
Gene: ENSMUSG00000030742

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

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 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

Predicted Effect

probably benign
Transcript: ENSMUST00000205366

Predicted Effect

probably null
Transcript: ENSMUST00000205642

Predicted Effect

probably null
Transcript: ENSMUST00000205642

Predicted Effect

probably null
Transcript: ENSMUST00000205642

Predicted Effect

probably benign
Transcript: ENSMUST00000205930

Predicted Effect

probably null
Transcript: ENSMUST00000206793

Predicted Effect

probably null
Transcript: ENSMUST00000206793

Predicted Effect

probably null
Transcript: ENSMUST00000206793

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (87/87)

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: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610021A01Rik	T	C	7: 41,275,554 (GRCm39)	I419T	possibly damaging	Het
Afap1	T	C	5: 36,119,604 (GRCm39)	V294A	probably benign	Het
Amotl1	T	A	9: 14,486,532 (GRCm39)	Q454L	possibly damaging	Het
Ap2a1	T	C	7: 44,550,215 (GRCm39)	S961G	probably damaging	Het
Asxl3	A	G	18: 22,650,731 (GRCm39)	K907E	probably damaging	Het
BC028528	A	T	3: 95,792,323 (GRCm39)	L137I	possibly damaging	Het
Cand1	A	T	10: 119,047,659 (GRCm39)	N610K	probably benign	Het
Cat	A	G	2: 103,304,698 (GRCm39)	I109T	probably benign	Het
Ccdc18	T	C	5: 108,341,664 (GRCm39)	V853A	probably benign	Het
Chd4	C	A	6: 125,085,405 (GRCm39)	D805E	possibly damaging	Het
Cnih1	A	C	14: 47,017,652 (GRCm39)	F77V	probably damaging	Het
Cntd1	A	T	11: 101,178,252 (GRCm39)	I284F	probably damaging	Het
Col6a3	C	A	1: 90,755,759 (GRCm39)	E177*	probably null	Het
Cpxm2	T	A	7: 131,745,408 (GRCm39)	D139V	probably benign	Het
Cyp1a2	G	T	9: 57,584,525 (GRCm39)	R510S	probably damaging	Het
D2hgdh	T	C	1: 93,763,096 (GRCm39)	S294P	probably damaging	Het
Dchs1	A	G	7: 105,406,228 (GRCm39)	C2335R	probably benign	Het
Disc1	G	T	8: 125,977,724 (GRCm39)	C719F	probably damaging	Het
Dnah14	A	C	1: 181,525,614 (GRCm39)	D2180A	probably benign	Het
Dop1b	G	A	16: 93,573,878 (GRCm39)	R1582Q	probably benign	Het
Dsg2	A	T	18: 20,725,332 (GRCm39)	H481L	probably benign	Het
Epha6	A	G	16: 59,503,013 (GRCm39)	S965P	probably damaging	Het
Esrrg	G	T	1: 187,882,503 (GRCm39)	L253F	probably damaging	Het
Exoc6b	T	C	6: 84,831,704 (GRCm39)	K438R	probably damaging	Het
Fam98a	C	A	17: 75,845,384 (GRCm39)	R454L	unknown	Het
Fam98c	A	T	7: 28,855,308 (GRCm39)		probably null	Het
Fhad1	CGG	CG	4: 141,645,602 (GRCm39)		probably null	Het
Galnt13	A	G	2: 54,988,587 (GRCm39)	T470A	probably damaging	Het
Ggt7	A	T	2: 155,345,015 (GRCm39)		probably null	Het
Golim4	T	C	3: 75,785,957 (GRCm39)	E606G	probably damaging	Het
Gpd2	G	A	2: 57,197,112 (GRCm39)		probably null	Het
Grin2b	T	C	6: 135,757,304 (GRCm39)	M386V	probably damaging	Het
Hfm1	A	T	5: 107,059,306 (GRCm39)	S239T	probably benign	Het
Hmcn1	G	A	1: 150,649,641 (GRCm39)	T615I	probably benign	Het
Hook2	G	A	8: 85,724,040 (GRCm39)	E446K	possibly damaging	Het
Hsd3b1	C	T	3: 98,765,131 (GRCm39)		probably null	Het
Igsf9b	A	G	9: 27,234,150 (GRCm39)	Y421C	probably damaging	Het
Il21	A	G	3: 37,286,629 (GRCm39)	L29P	probably damaging	Het
Ildr1	A	G	16: 36,542,730 (GRCm39)	S421G	probably benign	Het
Kat2b	C	A	17: 53,972,894 (GRCm39)	T736K	probably benign	Het
Kcng1	A	G	2: 168,104,529 (GRCm39)	V439A	probably damaging	Het
Kif21a	A	T	15: 90,833,106 (GRCm39)		probably null	Het
Mastl	T	A	2: 23,023,425 (GRCm39)	K433*	probably null	Het
Mettl2	A	G	11: 105,019,719 (GRCm39)	R119G	probably benign	Het
Mia2	C	T	12: 59,231,021 (GRCm39)	P1223L	possibly damaging	Het
Mkrn2os	G	T	6: 115,563,635 (GRCm39)	D133E	probably benign	Het
Mslnl	A	G	17: 25,962,186 (GRCm39)	T195A	probably benign	Het
Muc16	T	G	9: 18,551,051 (GRCm39)	T5081P	probably benign	Het
Mylpf	G	C	7: 126,813,139 (GRCm39)	R110P	probably damaging	Het
Myo19	G	T	11: 84,798,194 (GRCm39)	C738F	possibly damaging	Het
Nat8f4	T	A	6: 85,878,271 (GRCm39)	N84I	possibly damaging	Het
Nol8	C	T	13: 49,829,862 (GRCm39)	R1104C	probably damaging	Het
Notch1	A	T	2: 26,353,830 (GRCm39)	D1932E	probably benign	Het
Nsun3	A	T	16: 62,596,663 (GRCm39)	C152S	possibly damaging	Het
Opcml	G	A	9: 28,586,507 (GRCm39)	W75*	probably null	Het
Or14j10	A	G	17: 37,934,597 (GRCm39)	F310L	probably benign	Het
Pcdh7	G	A	5: 57,879,582 (GRCm39)	E1046K	probably damaging	Het
Pcdhb9	T	A	18: 37,536,334 (GRCm39)	V776D	probably benign	Het
Pla2g4a	A	G	1: 149,727,103 (GRCm39)	L551S	probably damaging	Het
Plaa	G	A	4: 94,458,060 (GRCm39)	Q637*	probably null	Het
Plekhh1	A	T	12: 79,122,204 (GRCm39)	E1099V	probably damaging	Het
Ppp4r1	A	T	17: 66,136,495 (GRCm39)	N551Y	probably benign	Het
R3hdm2	T	C	10: 127,320,382 (GRCm39)	V554A	probably damaging	Het
Rab44	A	G	17: 29,357,150 (GRCm39)		probably null	Het
Rab5c	G	A	11: 100,610,789 (GRCm39)	R40C	probably damaging	Het
Rasgrf2	T	C	13: 92,034,521 (GRCm39)	T1119A	probably damaging	Het
Rims2	A	G	15: 39,449,044 (GRCm39)	D1194G	probably damaging	Het
Scarb1	A	T	5: 125,374,294 (GRCm39)	C280S	probably damaging	Het
Sde2	T	C	1: 180,693,827 (GRCm39)	F439S	probably damaging	Het
Setd5	T	C	6: 113,092,532 (GRCm39)	I304T	probably benign	Het
Sipa1l1	A	G	12: 82,449,896 (GRCm39)	E1106G	probably benign	Het
Sis	T	G	3: 72,810,940 (GRCm39)	S1694R	probably damaging	Het
Smad9	T	A	3: 54,693,614 (GRCm39)	F181Y	probably benign	Het
Smg1	A	G	7: 117,797,502 (GRCm39)		probably benign	Het
Sspo	T	C	6: 48,425,516 (GRCm39)	Y46H	probably damaging	Het
Tdrd12	A	G	7: 35,177,534 (GRCm39)	M940T	unknown	Het
Tmem44	G	T	16: 30,366,213 (GRCm39)	T71K	possibly damaging	Het
Tmf1	T	A	6: 97,133,911 (GRCm39)	E1009V	probably damaging	Het
Ttc39a	C	T	4: 109,288,763 (GRCm39)	R288W	probably damaging	Het
Ttc9c	G	A	19: 8,796,191 (GRCm39)		probably benign	Het
Usp28	T	A	9: 48,950,456 (GRCm39)	Y634N	probably damaging	Het
Vmn1r211	C	T	13: 23,036,063 (GRCm39)	M201I	probably benign	Het
Vmn2r54	T	A	7: 12,349,722 (GRCm39)	Q620L	possibly damaging	Het
Vps13c	T	C	9: 67,831,110 (GRCm39)	L1580P	probably benign	Het
Vrk3	C	A	7: 44,417,890 (GRCm39)	F308L	probably damaging	Het
Zdbf2	T	A	1: 63,346,563 (GRCm39)	H1647Q	possibly damaging	Het
Zfp984	A	T	4: 147,840,002 (GRCm39)	M283K	probably benign	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
R2215:Lat	UTSW	7	125,967,137 (GRCm39)	missense	probably damaging	1.00
R4947:Lat	UTSW	7	125,967,110 (GRCm39)	missense	probably benign	0.03
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'- AGTGCTGTCATAGGAGACTGG -3'
(R):5'- GAAAGGATACGGCTGCCTACTG -3'

Sequencing Primer
(F):5'- CTGGAGGAAAGAAATCCAACAAGTC -3'
(R):5'- AGCCCGCTTGGTCCCATAC -3'

Posted On

2019-05-13