Mutagenetix > Incidental Mutation

Incidental Mutation 'R3196:Lcp2'

267662

Institutional Source

Beutler Lab

Gene Symbol

Lcp2

Ensembl Gene

ENSMUSG00000002699

Gene Name

lymphocyte cytosolic protein 2

Synonyms

m1Khoe, SLP-76, SLP76, twm

MMRRC Submission

040617-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R3196 (G1)

Quality Score

202

Status

Not validated

Chromosome

Chromosomal Location

33996928-34042281 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 34040670 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Serine at position 529 (A529S)

Ref Sequence

ENSEMBL: ENSMUSP00000056621 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000052413] [ENSMUST00000109329] [ENSMUST00000223852] [ENSMUST00000224226]

AlphaFold

Q60787

Predicted Effect

probably benign
Transcript: ENSMUST00000052413
AA Change: A529S

PolyPhen 2 Score 0.055 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000056621
Gene: ENSMUSG00000002699
AA Change: A529S

Domain	Start	End	E-Value	Type
SAM	12	78	9.3e-4	SMART
low complexity region	109	127	N/A	INTRINSIC
low complexity region	186	201	N/A	INTRINSIC
low complexity region	204	222	N/A	INTRINSIC
internal_repeat_1	274	321	1.93e-5	PROSPERO
low complexity region	328	339	N/A	INTRINSIC
low complexity region	400	412	N/A	INTRINSIC
SH2	421	512	4.44e-25	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000109329

SMART Domains

Protein: ENSMUSP00000104952
Gene: ENSMUSG00000002699

Domain	Start	End	E-Value	Type
SAM	12	78	9.3e-4	SMART
low complexity region	109	127	N/A	INTRINSIC
low complexity region	186	201	N/A	INTRINSIC
low complexity region	204	222	N/A	INTRINSIC
internal_repeat_1	274	321	1.86e-5	PROSPERO
low complexity region	328	339	N/A	INTRINSIC
low complexity region	400	412	N/A	INTRINSIC
SH2	421	508	8.9e-16	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141450

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146318

Predicted Effect

probably benign
Transcript: ENSMUST00000169878
AA Change: A529S

PolyPhen 2 Score 0.055 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000126796
Gene: ENSMUSG00000002699
AA Change: A529S

Domain	Start	End	E-Value	Type
SAM	12	78	9.3e-4	SMART
low complexity region	109	127	N/A	INTRINSIC
low complexity region	186	201	N/A	INTRINSIC
low complexity region	204	222	N/A	INTRINSIC
internal_repeat_1	274	321	1.87e-5	PROSPERO
low complexity region	328	339	N/A	INTRINSIC
low complexity region	399	411	N/A	INTRINSIC
SH2	420	511	4.44e-25	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000223852

Predicted Effect

probably benign
Transcript: ENSMUST00000224226

Coding Region Coverage

1x: 99.1%
3x: 98.6%
10x: 97.3%
20x: 95.1%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an adapter protein that acts as a substrate of the T cell antigen receptor (TCR)-activated protein tyrosine kinase pathway. The encoded protein associates with growth factor receptor bound protein 2, and is thought to play a role TCR-mediated intracellular signal transduction. A similar protein in mouse plays a role in normal T-cell development and activation. Mice lacking this gene show subcutaneous and intraperitoneal fetal hemorrhaging, dysfunctional platelets and impaired viability. [provided by RefSeq, Nov 2016]
PHENOTYPE: T cell development is blocked and T cell receptor signaling impaired in homozygous point mutants. Double positive thymocyte and single positive T cell numbers are much reduced. Both positive and negative thymocyte selection is abnormal. Mice have high IgG and IgE levels and exhibit autoimmunity. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9130401M01Rik	A	T	15: 57,892,132 (GRCm39)	N158K	probably benign	Het
Acnat1	G	C	4: 49,447,457 (GRCm39)	P357A	probably damaging	Het
Akap6	T	A	12: 53,119,240 (GRCm39)	C1102*	probably null	Het
Amelx	T	C	X: 167,964,826 (GRCm39)		probably benign	Het
Brap	G	A	5: 121,803,259 (GRCm39)	V136I	possibly damaging	Het
Crygs	C	T	16: 22,624,301 (GRCm39)	G102D	possibly damaging	Het
Csgalnact1	TGG	TG	8: 68,913,737 (GRCm39)		probably null	Het
Csk	A	T	9: 57,537,556 (GRCm39)	C119*	probably null	Het
Dcbld1	T	C	10: 52,195,587 (GRCm39)	L265P	probably damaging	Het
Desi1	T	A	15: 81,887,976 (GRCm39)	K31N	probably damaging	Het
Dpy19l2	C	A	9: 24,607,285 (GRCm39)	G59C	probably damaging	Het
Eif2b5	T	C	16: 20,324,272 (GRCm39)	V498A	probably benign	Het
Epdr1	A	T	13: 19,778,815 (GRCm39)	Y94N	probably damaging	Het
Fat1	T	C	8: 45,404,905 (GRCm39)	V552A	probably benign	Het
Focad	A	G	4: 88,325,588 (GRCm39)	E151G	possibly damaging	Het
Frem1	A	G	4: 82,932,351 (GRCm39)	F117L	probably damaging	Het
Frem2	A	T	3: 53,444,752 (GRCm39)	Y2460N	probably damaging	Het
Gm3604	A	T	13: 62,517,868 (GRCm39)	C163*	probably null	Het
Gpalpp1	A	C	14: 76,336,063 (GRCm39)		probably null	Het
Grid2ip	A	G	5: 143,373,933 (GRCm39)	I858V	probably damaging	Het
Grin2b	ATTGTTGT	ATTGT	6: 135,709,453 (GRCm39)		probably benign	Het
Hps4	A	G	5: 112,512,429 (GRCm39)	T182A	probably damaging	Het
Impa1	A	T	3: 10,394,075 (GRCm39)		probably null	Het
Kcnh3	T	C	15: 99,131,862 (GRCm39)	S606P	probably damaging	Het
Kif23	T	A	9: 61,839,193 (GRCm39)	R301*	probably null	Het
Kirrel1	C	T	3: 86,996,458 (GRCm39)	M380I	probably null	Het
Lhx8	G	A	3: 154,035,925 (GRCm39)	A22V	probably benign	Het
Lin28a	A	T	4: 133,735,235 (GRCm39)	S134T	possibly damaging	Het
Med27	T	A	2: 29,236,882 (GRCm39)	V9E	possibly damaging	Het
Mmp7	C	A	9: 7,692,219 (GRCm39)	S31R	probably benign	Het
Mtcl1	T	G	17: 66,650,829 (GRCm39)	E1545D	probably benign	Het
Muc16	A	G	9: 18,409,126 (GRCm39)	Y187H	probably damaging	Het
Myo3a	G	T	2: 22,404,679 (GRCm39)	K678N	possibly damaging	Het
Nsmce1	T	C	7: 125,085,645 (GRCm39)	M15V	probably benign	Het
Nxpe3	A	T	16: 55,670,078 (GRCm39)	N342K	probably damaging	Het
Or7g25	A	G	9: 19,160,495 (GRCm39)	S67P	probably damaging	Het
Or8g2	T	A	9: 39,821,756 (GRCm39)	I219N	probably damaging	Het
Pcdhb9	A	G	18: 37,534,663 (GRCm39)	N219S	probably benign	Het
Pck2	T	A	14: 55,781,449 (GRCm39)	V190E	probably damaging	Het
Pde4b	G	A	4: 102,456,840 (GRCm39)	A429T	probably damaging	Het
Phf1	T	C	17: 27,153,429 (GRCm39)	V54A	probably damaging	Het
Pla2r1	T	C	2: 60,353,127 (GRCm39)	E278G	probably damaging	Het
Ptges3	G	T	10: 127,908,016 (GRCm39)	R122L	probably benign	Het
Rnpepl1	C	T	1: 92,844,881 (GRCm39)	T391I	probably damaging	Het
Rps6kb1	G	A	11: 86,397,633 (GRCm39)	A404V	probably benign	Het
Rrm2b	T	C	15: 37,945,391 (GRCm39)		probably null	Het
Sh3rf1	C	T	8: 61,679,321 (GRCm39)	P121L	probably benign	Het
Skint9	T	G	4: 112,248,148 (GRCm39)	I199L	probably benign	Het
Slc9b2	G	T	3: 135,042,290 (GRCm39)	R523L	probably benign	Het
Slco1c1	T	A	6: 141,477,174 (GRCm39)		probably null	Het
Stox2	T	C	8: 47,645,865 (GRCm39)	T532A	probably damaging	Het
Tbcel	A	G	9: 42,327,248 (GRCm39)	L385P	probably damaging	Het
Tle5	A	G	10: 81,401,474 (GRCm39)	N181D	probably benign	Het
Tmem268	G	A	4: 63,496,149 (GRCm39)		probably null	Het
Tns2	C	T	15: 102,017,369 (GRCm39)	R281C	probably damaging	Het
Top3a	G	A	11: 60,650,182 (GRCm39)	T122M	probably damaging	Het
Trav7n-4	G	A	14: 53,329,088 (GRCm39)	V33I	probably benign	Het
Ttn	T	G	2: 76,539,551 (GRCm39)	E26151D	possibly damaging	Het
Ttn	C	T	2: 76,687,228 (GRCm39)		probably benign	Het
Tyk2	A	G	9: 21,035,328 (GRCm39)	C195R	possibly damaging	Het
Ugt2b38	T	C	5: 87,558,078 (GRCm39)	K528E	probably damaging	Het
Usp28	T	A	9: 48,937,125 (GRCm39)	D483E	probably benign	Het
Vldlr	A	G	19: 27,220,554 (GRCm39)	D598G	probably damaging	Het
Vmn1r51	T	G	6: 90,106,498 (GRCm39)	I138S	probably damaging	Het
Vps13b	G	A	15: 35,869,541 (GRCm39)	A2682T	probably damaging	Het
Wac	T	A	18: 7,917,568 (GRCm39)	V346E	probably damaging	Het
Zdbf2	T	C	1: 63,347,579 (GRCm39)	V1986A	possibly damaging	Het

Other mutations in Lcp2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01451:Lcp2	APN	11	33,997,345 (GRCm39)	start gained	probably benign
IGL01730:Lcp2	APN	11	34,000,943 (GRCm39)	missense	possibly damaging	0.91
IGL02174:Lcp2	APN	11	34,000,966 (GRCm39)	splice site	probably benign
IGL02228:Lcp2	APN	11	33,997,424 (GRCm39)	missense	probably damaging	1.00
IGL02814:Lcp2	APN	11	34,021,033 (GRCm39)	missense	probably damaging	1.00
R0142:Lcp2	UTSW	11	34,032,418 (GRCm39)	missense	probably damaging	0.97
R0277:Lcp2	UTSW	11	34,004,322 (GRCm39)	missense	probably damaging	1.00
R0281:Lcp2	UTSW	11	34,019,854 (GRCm39)	splice site	probably benign
R0323:Lcp2	UTSW	11	34,004,322 (GRCm39)	missense	probably damaging	1.00
R0437:Lcp2	UTSW	11	34,037,229 (GRCm39)	missense	probably benign	0.00
R0632:Lcp2	UTSW	11	34,032,426 (GRCm39)	missense	possibly damaging	0.87
R1479:Lcp2	UTSW	11	34,025,068 (GRCm39)	missense	probably benign	0.01
R1570:Lcp2	UTSW	11	34,039,601 (GRCm39)	missense	probably benign	0.07
R1744:Lcp2	UTSW	11	34,019,911 (GRCm39)	splice site	probably null
R2212:Lcp2	UTSW	11	34,020,995 (GRCm39)	missense	probably benign	0.14
R2910:Lcp2	UTSW	11	34,018,970 (GRCm39)	splice site	probably null
R2911:Lcp2	UTSW	11	34,018,970 (GRCm39)	splice site	probably null
R4012:Lcp2	UTSW	11	34,018,439 (GRCm39)	missense	probably damaging	1.00
R4411:Lcp2	UTSW	11	34,037,173 (GRCm39)	unclassified	probably benign
R4417:Lcp2	UTSW	11	34,000,917 (GRCm39)	missense	probably benign	0.27
R4423:Lcp2	UTSW	11	34,028,226 (GRCm39)	intron	probably benign
R4718:Lcp2	UTSW	11	34,020,992 (GRCm39)	missense	probably benign	0.09
R5090:Lcp2	UTSW	11	34,039,725 (GRCm39)	nonsense	probably null
R6347:Lcp2	UTSW	11	34,032,501 (GRCm39)	missense	probably benign	0.10
R7315:Lcp2	UTSW	11	34,019,906 (GRCm39)	critical splice donor site	probably null
R7694:Lcp2	UTSW	11	34,000,924 (GRCm39)	missense	probably benign	0.16
R7910:Lcp2	UTSW	11	34,038,061 (GRCm39)	missense	probably damaging	1.00
R8325:Lcp2	UTSW	11	34,032,394 (GRCm39)	missense	probably benign	0.34
R8435:Lcp2	UTSW	11	34,004,316 (GRCm39)	missense	probably damaging	1.00
R8709:Lcp2	UTSW	11	34,004,354 (GRCm39)	critical splice donor site	probably benign
R9091:Lcp2	UTSW	11	34,039,688 (GRCm39)	missense
R9270:Lcp2	UTSW	11	34,039,688 (GRCm39)	missense
R9566:Lcp2	UTSW	11	34,000,944 (GRCm39)	missense

Predicted Primers

PCR Primer
(F):5'- GAGGAGGAAATCTCTAAACTACCTG -3'
(R):5'- TCTGCCATGCACTCTTAGAC -3'

Sequencing Primer
(F):5'- ACCTGATAAATGCGTACTGTCC -3'
(R):5'- GCCATGCACTCTTAGACTTCAAATG -3'

Posted On

2015-02-18