Mutagenetix > Incidental Mutation

Incidental Mutation 'R3911:Lsp1'

309395

Institutional Source

Beutler Lab

Gene Symbol

Lsp1

Ensembl Gene

ENSMUSG00000018819

Gene Name

lymphocyte specific 1

Synonyms

WP34, leukocyte specific protein 1, pp52, leukocyte-specific protein 1, lymphocyte-specific protein 1, Lsp-1, p50

MMRRC Submission

040909-MU

Accession Numbers

Essential gene?

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

Stock #

R3911 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

142014583-142048605 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 142040098 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Phenylalanine at position 75 (S75F)

Ref Sequence

ENSEMBL: ENSMUSP00000040637 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000018963] [ENSMUST00000038946] [ENSMUST00000105966] [ENSMUST00000105967] [ENSMUST00000105968] [ENSMUST00000140626] [ENSMUST00000149521]

AlphaFold

P19973

Predicted Effect

probably damaging
Transcript: ENSMUST00000018963
AA Change: S77F

PolyPhen 2 Score 0.960 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000018963
Gene: ENSMUSG00000018819
AA Change: S77F

Domain	Start	End	E-Value	Type
coiled coil region	29	53	N/A	INTRINSIC
Pfam:Caldesmon	173	303	2.3e-32	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000038946
AA Change: S75F

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000040637
Gene: ENSMUSG00000018819
AA Change: S75F

Domain	Start	End	E-Value	Type
coiled coil region	27	51	N/A	INTRINSIC
Pfam:Caldesmon	171	301	2.3e-32	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000054910

SMART Domains

Protein: ENSMUSP00000061994
Gene: ENSMUSG00000043795

Domain	Start	End	E-Value	Type
Pfam:DUF4643	6	259	1.3e-108	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000105966
AA Change: S75F

PolyPhen 2 Score 0.960 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000101586
Gene: ENSMUSG00000018819
AA Change: S75F

Domain	Start	End	E-Value	Type
coiled coil region	27	51	N/A	INTRINSIC
Pfam:Caldesmon	166	294	6.4e-32	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000105967
AA Change: S77F

PolyPhen 2 Score 0.960 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000101587
Gene: ENSMUSG00000018819
AA Change: S77F

Domain	Start	End	E-Value	Type
coiled coil region	29	53	N/A	INTRINSIC
Pfam:Caldesmon	168	296	6.7e-32	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000105968
AA Change: S77F

PolyPhen 2 Score 0.960 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000101588
Gene: ENSMUSG00000018819
AA Change: S77F

Domain	Start	End	E-Value	Type
coiled coil region	29	53	N/A	INTRINSIC
Pfam:Caldesmon	173	280	9.3e-29	PFAM
low complexity region	291	307	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126149

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156960

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128986

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132956

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142408

Predicted Effect

probably benign
Transcript: ENSMUST00000140626

Predicted Effect

probably benign
Transcript: ENSMUST00000149521

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.0%

Validation Efficiency

100% (71/71)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an intracellular F-actin binding protein. The protein is expressed in lymphocytes, neutrophils, macrophages, and endothelium and may regulate neutrophil motility, adhesion to fibrinogen matrix proteins, and transendothelial migration. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit increased numbers of resident peritoneal macrophages and reduced numbers of peritoneal lymphocytes. Mutant neutrophils show abnormal morphology and impaired chemokine-induced migration. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb9	T	A	5: 124,227,909 (GRCm39)	I111F	probably benign	Het
Abcc12	A	C	8: 87,255,048 (GRCm39)		probably benign	Het
Adgre1	G	T	17: 57,754,860 (GRCm39)	V653L	probably damaging	Het
Aebp2	T	A	6: 140,593,707 (GRCm39)	D230E	probably damaging	Het
Asap3	A	G	4: 135,956,768 (GRCm39)		probably benign	Het
Bod1l	T	C	5: 41,974,441 (GRCm39)	E2291G	probably damaging	Het
Casp8	A	T	1: 58,872,864 (GRCm39)	S267C	probably damaging	Het
Cchcr1	T	C	17: 35,836,233 (GRCm39)	V341A	probably damaging	Het
Cd2ap	T	A	17: 43,126,980 (GRCm39)		probably null	Het
Cimip3	AC	A	17: 47,744,348 (GRCm39)		probably benign	Het
Clip1	T	A	5: 123,728,897 (GRCm39)	E1155D	probably damaging	Het
Cnnm2	A	G	19: 46,866,375 (GRCm39)	E841G	probably damaging	Het
Cntrl	G	A	2: 35,010,061 (GRCm39)	R245H	probably damaging	Het
Cyp2b23	A	T	7: 26,380,842 (GRCm39)	S128T	probably benign	Het
Dhrs11	A	T	11: 84,712,579 (GRCm39)	I196N	probably damaging	Het
Dnah17	C	T	11: 117,971,675 (GRCm39)		probably benign	Het
Edc3	A	T	9: 57,655,686 (GRCm39)	I479F	possibly damaging	Het
Emg1	T	A	6: 124,682,009 (GRCm39)	M172L	probably benign	Het
Epha7	G	A	4: 28,938,680 (GRCm39)	V512I	probably benign	Het
Exoc7	T	C	11: 116,197,731 (GRCm39)	D27G	probably benign	Het
Fasl	C	A	1: 161,615,760 (GRCm39)	C32F	probably benign	Het
Flg	A	T	3: 93,187,307 (GRCm39)	H253L	probably benign	Het
Fnip2	A	T	3: 79,386,812 (GRCm39)	D971E	possibly damaging	Het
Gab2	A	G	7: 96,948,280 (GRCm39)	Y290C	probably damaging	Het
Gm17067	T	A	7: 42,360,104 (GRCm39)	I43L	possibly damaging	Het
Gpld1	A	G	13: 25,146,305 (GRCm39)	Y183C	probably damaging	Het
Gpr137c	C	A	14: 45,516,392 (GRCm39)	P327T	probably benign	Het
Hepacam2	A	G	6: 3,494,477 (GRCm39)	M1T	probably null	Het
Ighv5-4	A	T	12: 113,561,060 (GRCm39)		probably benign	Het
Iqca1l	A	T	5: 24,750,440 (GRCm39)		probably benign	Het
Itgb8	T	A	12: 119,131,740 (GRCm39)	E635V	possibly damaging	Het
Kat14	T	C	2: 144,245,982 (GRCm39)	V469A	probably damaging	Het
Kcnj15	C	T	16: 95,097,329 (GRCm39)	T317I	probably damaging	Het
Kirrel1	C	T	3: 86,996,458 (GRCm39)	M380I	probably null	Het
Klhl18	A	T	9: 110,265,151 (GRCm39)	L285Q	probably damaging	Het
Krt90	G	A	15: 101,471,218 (GRCm39)	R15W	probably damaging	Het
Krtap4-8	A	T	11: 99,670,863 (GRCm39)	C203S	unknown	Het
Map1b	A	G	13: 99,567,580 (GRCm39)	S1714P	unknown	Het
Mcm2	A	G	6: 88,865,234 (GRCm39)	I481T	probably damaging	Het
Mcpt9	T	C	14: 56,265,136 (GRCm39)	T122A	probably benign	Het
Megf10	A	T	18: 57,422,465 (GRCm39)	R947W	probably damaging	Het
Or2ag18	A	T	7: 106,405,072 (GRCm39)	V199D	probably damaging	Het
Or51ai2	A	T	7: 103,586,616 (GRCm39)	N10Y	possibly damaging	Het
Pank4	A	G	4: 155,054,058 (GRCm39)	Y79C	probably damaging	Het
Pds5b	T	A	5: 150,670,171 (GRCm39)	N386K	probably benign	Het
Pfkm	A	G	15: 98,022,928 (GRCm39)	M362V	probably benign	Het
Phc2	T	C	4: 128,637,351 (GRCm39)		probably null	Het
Pou4f1	C	T	14: 104,703,611 (GRCm39)	A274T	unknown	Het
Proc	A	G	18: 32,256,758 (GRCm39)	L303P	probably damaging	Het
Ptk2b	C	T	14: 66,394,517 (GRCm39)	G821D	possibly damaging	Het
Rlim	T	C	X: 103,006,267 (GRCm39)	T545A	probably benign	Het
Serpinb6c	T	C	13: 34,077,888 (GRCm39)	N161D	probably benign	Het
Sf3b1	G	A	1: 55,058,548 (GRCm39)	Q14*	probably null	Het
Sh3d19	G	A	3: 86,014,534 (GRCm39)	V442M	possibly damaging	Het
Slc30a8	A	G	15: 52,185,097 (GRCm39)	I140V	probably benign	Het
Spata1	T	A	3: 146,181,079 (GRCm39)	N293I	probably damaging	Het
Strap	T	G	6: 137,712,380 (GRCm39)	C10G	probably damaging	Het
Tcf7	C	A	11: 52,173,793 (GRCm39)		probably benign	Het
Tmem114	A	T	16: 8,230,054 (GRCm39)	M116K	probably damaging	Het
Tmem63b	A	G	17: 45,988,884 (GRCm39)	S113P	probably damaging	Het
Tmtc3	A	C	10: 100,284,888 (GRCm39)	N582K	probably damaging	Het
Tnfrsf11b	G	A	15: 54,119,578 (GRCm39)		probably benign	Het
Tns2	T	C	15: 102,022,272 (GRCm39)		probably null	Het
Trim30a	A	G	7: 104,060,348 (GRCm39)	V476A	probably damaging	Het
Ush2a	T	A	1: 188,132,151 (GRCm39)	V791D	probably benign	Het
Vmn2r99	T	C	17: 19,614,635 (GRCm39)	F785S	possibly damaging	Het
Vps35l	A	G	7: 118,345,613 (GRCm39)	T49A	possibly damaging	Het
Wdr35	A	T	12: 9,036,077 (GRCm39)	I283F	probably benign	Het
Wnt10b	G	T	15: 98,672,219 (GRCm39)	A166E	possibly damaging	Het

Other mutations in Lsp1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02351:Lsp1	APN	7	142,042,679 (GRCm39)	critical splice donor site	probably null
IGL02358:Lsp1	APN	7	142,042,679 (GRCm39)	critical splice donor site	probably null
IGL02624:Lsp1	APN	7	142,044,288 (GRCm39)	splice site	probably benign
R0594:Lsp1	UTSW	7	142,042,687 (GRCm39)	splice site	probably benign
R0603:Lsp1	UTSW	7	142,043,115 (GRCm39)	missense	probably damaging	1.00
R2055:Lsp1	UTSW	7	142,043,144 (GRCm39)	critical splice donor site	probably null
R2090:Lsp1	UTSW	7	142,045,544 (GRCm39)	intron	probably benign
R5965:Lsp1	UTSW	7	142,044,161 (GRCm39)	critical splice donor site	probably null
R7186:Lsp1	UTSW	7	142,044,089 (GRCm39)	missense	probably damaging	1.00
R7216:Lsp1	UTSW	7	142,042,179 (GRCm39)	missense	probably damaging	1.00
R9665:Lsp1	UTSW	7	142,044,142 (GRCm39)	missense	probably benign	0.02

Predicted Primers

PCR Primer
(F):5'- CGAACACAATGCTGTTCTCAGG -3'
(R):5'- AAAGAGATCCAGTGCCTTGGTTC -3'

Sequencing Primer
(F):5'- CAATGCTGTTCTCAGGAAGCTATAGG -3'
(R):5'- AGTGCCTTGGTTCACACTTG -3'

Posted On

2015-04-17