Mutagenetix > Incidental Mutation

Incidental Mutation 'R6422:Lat2'

518208

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

044563-MU

Accession Numbers

Essential gene?

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

Stock #

R6422 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

134628876-134643879 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 134632015 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 144 (D144G)

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: D156G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000046900
Gene: ENSMUSG00000040751
AA Change: D156G

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: D144G

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000076824
Gene: ENSMUSG00000040751
AA Change: D144G

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

Predicted Effect

silent
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: D156G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000143977
Gene: ENSMUSG00000040751
AA Change: D156G

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: D53G

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000202461

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201832

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000202746

Meta Mutation Damage Score

0.0846

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.5%
20x: 91.8%

Validation Efficiency

97% (30/31)

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: 31 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A430005L14Rik	T	A	4: 154,045,381 (GRCm39)	F137I	probably damaging	Het
Adam11	A	G	11: 102,665,109 (GRCm39)	K417R	possibly damaging	Het
Btbd9	G	A	17: 30,749,230 (GRCm39)	A28V	probably benign	Het
Cabin1	A	G	10: 75,492,626 (GRCm39)	Y1890H	probably damaging	Het
Castor2	T	A	5: 134,164,549 (GRCm39)	M170K	probably benign	Het
Cep162	G	T	9: 87,114,069 (GRCm39)	N334K	possibly damaging	Het
Cep85l	A	T	10: 53,167,876 (GRCm39)	M634K	possibly damaging	Het
Col20a1	C	A	2: 180,656,612 (GRCm39)	T1161N	possibly damaging	Het
Dip2b	T	A	15: 100,096,892 (GRCm39)	D1155E	probably damaging	Het
Dlst	T	A	12: 85,177,659 (GRCm39)		probably null	Het
Dsc1	A	C	18: 20,228,090 (GRCm39)	L422R	probably damaging	Het
Gcn1	T	C	5: 115,747,603 (GRCm39)	W1699R	probably damaging	Het
Gm14443	G	A	2: 175,012,174 (GRCm39)	Q91*	probably null	Het
Gm8159	T	C	14: 15,850,210 (GRCm39)	I143T	probably damaging	Het
Il4i1	G	T	7: 44,489,560 (GRCm39)	A442S	probably damaging	Het
Kif26a	T	G	12: 112,135,309 (GRCm39)	L337R	possibly damaging	Het
Ndst1	G	T	18: 60,836,025 (GRCm39)	H419Q	probably benign	Het
Notch4	T	C	17: 34,803,533 (GRCm39)	I1484T	probably benign	Het
Or51v14	T	G	7: 103,261,221 (GRCm39)	E113A	probably damaging	Het
Paxbp1	A	T	16: 90,820,332 (GRCm39)	M697K	probably benign	Het
Plxnb1	A	G	9: 108,937,992 (GRCm39)	Y1246C	probably damaging	Het
Prr5	C	T	15: 84,578,005 (GRCm39)	R96C	probably damaging	Het
Ptpn7	G	T	1: 135,062,240 (GRCm39)	C62F	probably damaging	Het
Rsrc1	C	T	3: 66,901,982 (GRCm39)	P44L	unknown	Het
Sall2	A	C	14: 52,550,181 (GRCm39)	*1003G	probably null	Het
Slc5a4b	C	A	10: 75,939,696 (GRCm39)	V147F	probably damaging	Het
Snapc4	A	G	2: 26,258,315 (GRCm39)	W702R	probably benign	Het
Tbc1d32	A	T	10: 55,904,157 (GRCm39)	C1203*	probably null	Het
Tmprss11d	T	A	5: 86,457,284 (GRCm39)	Y125F	probably damaging	Het
Tpp1	G	A	7: 105,396,163 (GRCm39)	T512I	probably benign	Het
Tyw5	G	A	1: 57,440,570 (GRCm39)	A64V	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
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
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'- CACTGTGAAGTGAGCCAGAC -3'
(R):5'- TGAGCTAGACCCACCCTAATG -3'

Sequencing Primer
(F):5'- CTGTGAAGTGAGCCAGACTAGATAG -3'
(R):5'- GGAGGTCCCCAAGATTCTAAATC -3'

Posted On

2018-05-24