Mutagenetix > Incidental Mutation

Incidental Mutation 'R1013:Lck'

95854

Institutional Source

Beutler Lab

Gene Symbol

Lck

Ensembl Gene

ENSMUSG00000000409

Gene Name

lymphocyte protein tyrosine kinase

Synonyms

Hck-3, p56

MMRRC Submission

039117-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1013 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

129442142-129467415 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 129451920 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Tyrosine at position 20 (C20Y)

Ref Sequence

ENSEMBL: ENSMUSP00000119263 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000067240] [ENSMUST00000102596] [ENSMUST00000134336] [ENSMUST00000167288]

AlphaFold

P06240

Predicted Effect

probably damaging
Transcript: ENSMUST00000067240
AA Change: C20Y

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

SMART Domains

Protein: ENSMUSP00000066209
Gene: ENSMUSG00000000409
AA Change: C20Y

Domain	Start	End	E-Value	Type
SH3	64	120	3.53e-17	SMART
SH2	125	215	2.07e-34	SMART
TyrKc	245	494	2.66e-133	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000102596
AA Change: C20Y

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

SMART Domains

Protein: ENSMUSP00000099656
Gene: ENSMUSG00000000409
AA Change: C20Y

Domain	Start	End	E-Value	Type
SH3	64	120	3.53e-17	SMART
SH2	125	215	2.07e-34	SMART
TyrKc	245	494	2.66e-133	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000123640

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127943

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132030

Predicted Effect

probably damaging
Transcript: ENSMUST00000134336
AA Change: C20Y

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

SMART Domains

Protein: ENSMUSP00000119263
Gene: ENSMUSG00000000409
AA Change: C20Y

Domain	Start	End	E-Value	Type
PDB:1Q69\|B	7	33	9e-12	PDB
SCOP:d1awj__	45	92	2e-8	SMART
PDB:1LCK\|A	53	92	3e-20	PDB
Blast:SH3	64	92	4e-13	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139957

Predicted Effect

probably damaging
Transcript: ENSMUST00000167288
AA Change: C31Y

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

SMART Domains

Protein: ENSMUSP00000125777
Gene: ENSMUSG00000000409
AA Change: C31Y

Domain	Start	End	E-Value	Type
SH3	75	131	3.53e-17	SMART
SH2	136	226	2.07e-34	SMART
TyrKc	256	505	2.66e-133	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000183371

Meta Mutation Damage Score

0.9413

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.1%
20x: 91.4%

Validation Efficiency

98% (39/40)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the Src family of protein tyrosine kinases (PTKs). The encoded protein is a key signaling molecule in the selection and maturation of developing T-cells. It contains N-terminal sites for myristylation and palmitylation, a PTK domain, and SH2 and SH3 domains which are involved in mediating protein-protein interactions with phosphotyrosine-containing and proline-rich motifs, respectively. The protein localizes to the plasma membrane and pericentrosomal vesicles, and binds to cell surface receptors, including CD4 and CD8, and other signaling molecules. Multiple alternatively spliced variants encoding different isoforms have been described. [provided by RefSeq, Aug 2016]
PHENOTYPE: Mice homozygous for mutations of this gene exhibit thymic atrophy with reduced numbers of peripheral T cells. Null mutants have few double positive and no mature single positive (SP) thymocytes. A hypomorph has decreased expression of CD3epsilon chain onSP thymocytes, whose numbers are reduced. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 34 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700056E22Rik	C	T	1: 183,765,702 (GRCm39)	S119N	probably benign	Het
4930527J03Rik	ACCC	ACC	1: 178,276,503 (GRCm38)		noncoding transcript	Het
Bclaf1	T	A	10: 20,207,822 (GRCm39)		probably benign	Het
Bicdl2	A	G	17: 23,884,377 (GRCm39)		probably benign	Het
C8a	T	C	4: 104,685,236 (GRCm39)	I336V	probably benign	Het
Calcr	A	T	6: 3,692,621 (GRCm39)	V374D	probably damaging	Het
Col28a1	A	G	6: 7,999,452 (GRCm39)		probably benign	Het
Cuedc1	C	T	11: 88,078,853 (GRCm39)	A327V	possibly damaging	Het
Cul2	C	A	18: 3,425,535 (GRCm39)	Y378*	probably null	Het
Dnaaf10	A	G	11: 17,178,183 (GRCm39)	K226E	probably damaging	Het
Flt4	C	T	11: 49,527,166 (GRCm39)		probably benign	Het
Gm8369	TG	TGNG	19: 11,489,147 (GRCm39)		probably null	Het
Hivep1	A	G	13: 42,310,438 (GRCm39)	R893G	probably damaging	Het
Il10rb	A	G	16: 91,211,581 (GRCm39)	N140D	probably benign	Het
Itga4	A	G	2: 79,150,847 (GRCm39)	M818V	probably benign	Het
Kyat3	T	C	3: 142,432,007 (GRCm39)	I245T	probably damaging	Het
Mcm6	T	G	1: 128,276,778 (GRCm39)	S271R	probably benign	Het
Megf10	A	G	18: 57,394,291 (GRCm39)	I472V	probably benign	Het
Mroh2a	T	C	1: 88,162,334 (GRCm39)		probably null	Het
Mrpl11	T	C	19: 5,013,651 (GRCm39)	I144T	possibly damaging	Het
Or2t26	G	A	11: 49,039,977 (GRCm39)	V298M	probably damaging	Het
Or8k25	G	A	2: 86,244,319 (GRCm39)	P26S	possibly damaging	Het
Pcdhb17	A	G	18: 37,619,020 (GRCm39)	D270G	probably damaging	Het
Plg	G	A	17: 12,597,608 (GRCm39)		probably benign	Het
Ppp3cb	T	A	14: 20,574,072 (GRCm39)	E255D	probably benign	Het
Psenen	A	G	7: 30,261,802 (GRCm39)	F38S	possibly damaging	Het
Rims4	C	T	2: 163,705,849 (GRCm39)	V262M	possibly damaging	Het
Sorl1	T	C	9: 41,913,855 (GRCm39)	N1358S	probably benign	Het
Trim3	G	A	7: 105,267,102 (GRCm39)	P426S	probably benign	Het
Ttc28	T	C	5: 111,424,831 (GRCm39)	M1552T	probably benign	Het
Unc13c	T	C	9: 73,840,614 (GRCm39)	D79G	probably benign	Het
Zcchc14	A	G	8: 122,333,664 (GRCm39)		probably benign	Het
Zfp354a	T	C	11: 50,951,677 (GRCm39)		probably benign	Het
Zfp729a	T	C	13: 67,767,626 (GRCm39)	I868V	probably benign	Het

Other mutations in Lck

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01824:Lck	APN	4	129,451,939 (GRCm39)	missense	probably benign	0.00
IGL02666:Lck	APN	4	129,450,212 (GRCm39)	missense	probably damaging	0.98
iconoclast	UTSW	4	129,449,397 (GRCm39)	missense	probably damaging	1.00
lockdown	UTSW	4	129,451,920 (GRCm39)	missense	probably damaging	1.00
stromberg	UTSW	4	129,449,433 (GRCm39)	missense	probably damaging	1.00
studentenkarzer	UTSW	4	129,450,098 (GRCm39)	missense	probably damaging	1.00
swan	UTSW	4	129,449,433 (GRCm39)	missense	probably damaging	1.00
R0091:Lck	UTSW	4	129,449,474 (GRCm39)	missense	possibly damaging	0.88
R0480:Lck	UTSW	4	129,449,433 (GRCm39)	missense	probably damaging	1.00
R1510:Lck	UTSW	4	129,449,461 (GRCm39)	missense	possibly damaging	0.92
R1569:Lck	UTSW	4	129,449,449 (GRCm39)	missense	probably damaging	0.98
R1845:Lck	UTSW	4	129,451,879 (GRCm39)	missense	probably benign	0.00
R2001:Lck	UTSW	4	129,442,730 (GRCm39)	missense	probably benign	0.00
R2141:Lck	UTSW	4	129,442,713 (GRCm39)	missense	probably damaging	1.00
R4694:Lck	UTSW	4	129,442,765 (GRCm39)	missense	possibly damaging	0.66
R4737:Lck	UTSW	4	129,449,777 (GRCm39)	missense	possibly damaging	0.93
R5706:Lck	UTSW	4	129,445,431 (GRCm39)	critical splice acceptor site	probably null
R5712:Lck	UTSW	4	129,450,103 (GRCm39)	missense	probably benign
R7023:Lck	UTSW	4	129,442,658 (GRCm39)	missense	possibly damaging	0.89
R7411:Lck	UTSW	4	129,445,763 (GRCm39)	missense	probably benign	0.02
R9044:Lck	UTSW	4	129,450,098 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGAGTGCTGCTATTTTCCAGAGCC -3'
(R):5'- GGAACCCAGTCAGGAGCTTGAATC -3'

Sequencing Primer
(F):5'- CCAGAGCCTTTAGTTATGGTCC -3'
(R):5'- TCAGGAGCTTGAATCCCACG -3'

Posted On

2014-01-05