Mutagenetix > Incidental Mutation

Incidental Mutation 'R5888:Lair1'

501619

Institutional Source

Beutler Lab

Gene Symbol

Lair1

Ensembl Gene

ENSMUSG00000055541

Gene Name

leukocyte-associated Ig-like receptor 1

Synonyms

mLair-1, Lair-1, 5133400O11Rik, D7Bwg0421e

MMRRC Submission

044089-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5888 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

4003402-4063204 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 4010845 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 134 (D134E)

Ref Sequence

ENSEMBL: ENSMUSP00000083589 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000068865] [ENSMUST00000086400] [ENSMUST00000086401] [ENSMUST00000108600] [ENSMUST00000131126] [ENSMUST00000136616] [ENSMUST00000149395] [ENSMUST00000205296]

AlphaFold

Q8BG84

Predicted Effect

possibly damaging
Transcript: ENSMUST00000068865
AA Change: D24E

PolyPhen 2 Score 0.805 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000070712
Gene: ENSMUSG00000055541
AA Change: D24E

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC
transmembrane domain	33	55	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000086400
AA Change: D134E

PolyPhen 2 Score 0.962 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000083588
Gene: ENSMUSG00000055541
AA Change: D134E

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC
PDB:4ETY\|D	22	134	5e-79	PDB
SCOP:d1nkr_2	24	118	2e-9	SMART
Blast:IG	38	119	9e-27	BLAST
transmembrane domain	143	165	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000086401
AA Change: D134E

PolyPhen 2 Score 0.962 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000083589
Gene: ENSMUSG00000055541
AA Change: D134E

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC
PDB:4ETY\|D	22	134	1e-78	PDB
SCOP:d1nkr_2	24	118	2e-9	SMART
Blast:IG	38	119	2e-26	BLAST
transmembrane domain	143	165	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000108600

SMART Domains

Protein: ENSMUSP00000104241
Gene: ENSMUSG00000055541

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC
PDB:4ETY\|D	22	133	8e-79	PDB
SCOP:d1nkr_2	24	118	1e-9	SMART
Blast:IG	38	119	6e-27	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000131126

SMART Domains

Protein: ENSMUSP00000121738
Gene: ENSMUSG00000055541

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000136616

SMART Domains

Protein: ENSMUSP00000122037
Gene: ENSMUSG00000055541

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000149395

SMART Domains

Protein: ENSMUSP00000116800
Gene: ENSMUSG00000055541

Domain	Start	End	E-Value	Type
signal peptide	1	21	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000205296

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206445

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.2%
20x: 94.9%

Validation Efficiency

94% (96/102)

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 an inhibitory receptor found on peripheral mononuclear cells, including natural killer cells, T cells, and B cells. Inhibitory receptors regulate the immune response to prevent lysis of cells recognized as self. The gene is a member of both the immunoglobulin superfamily and the leukocyte-associated inhibitory receptor family. The gene maps to a region of 19q13.4 called the leukocyte receptor cluster, which contains at least 29 genes encoding leukocyte-expressed receptors of the immunoglobulin superfamily. The encoded protein has been identified as an anchor for tyrosine phosphatase SHP-1, and may induce cell death in myeloid leukemias. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
PHENOTYPE: Mice homozygous for a knock-out allele are healthy and of normal longevity but show increased numbers of splenic B, regulatory T, and dendritic cells, and eosinophilia at a young age. Aging homozygotes display a higher frequency of activated and effector/memory T cells and a decreased IgG1 level. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700029P11Rik	T	C	15: 81,980,671	S38P	probably benign	Het
Adcy1	T	A	11: 7,139,095	V503E	possibly damaging	Het
Alk	C	A	17: 71,874,943	V1362L	probably damaging	Het
Ankrd55	T	A	13: 112,355,919	I208N	possibly damaging	Het
Asap2	T	A	12: 21,218,190	I319N	probably damaging	Het
Atp11b	T	C	3: 35,837,547	I1036T	probably benign	Het
B4gat1	T	C	19: 5,039,532	F186L	probably benign	Het
C3	T	A	17: 57,214,831	T1079S	probably damaging	Het
Cacul1	G	T	19: 60,537,464	T287K	possibly damaging	Het
Cbr3	G	C	16: 93,690,726	G266R	probably damaging	Het
Cd63	T	A	10: 128,912,291		probably null	Het
Chd7	G	A	4: 8,866,382	M851I	probably damaging	Het
Chst13	T	A	6: 90,309,572	H136L	probably benign	Het
Cyp2d22	T	C	15: 82,373,813	T179A	probably benign	Het
Dclre1b	A	T	3: 103,803,737	V286E	probably damaging	Het
Defb45	G	A	2: 152,593,234		probably benign	Het
Dlg1	T	C	16: 31,791,886		probably null	Het
Dock3	A	G	9: 107,023,803	V321A	probably benign	Het
Dytn	A	T	1: 63,677,237	V59E	possibly damaging	Het
Eif2ak1	A	G	5: 143,886,915	I393M	probably damaging	Het
Fam83g	A	T	11: 61,702,594	E318V	probably benign	Het
Fbxo34	T	A	14: 47,529,719	F179I	probably damaging	Het
Fmo5	T	A	3: 97,641,725	Y230N	probably benign	Het
Fzd9	T	G	5: 135,249,463		probably null	Het
Gata2	T	C	6: 88,200,740	S251P	probably benign	Het
Gigyf1	A	G	5: 137,525,697	D1043G	probably damaging	Het
Gm10260	G	A	13: 97,760,393	R66*	probably null	Het
Gm10322	T	A	10: 59,616,303	S81T	probably benign	Het
Gm11639	T	C	11: 104,721,401		probably benign	Het
Gm15517	A	T	7: 44,260,642		probably benign	Het
Haus4	T	C	14: 54,544,219	T232A	probably benign	Het
Hgfac	A	T	5: 35,045,407	H417L	probably damaging	Het
Iqgap2	T	C	13: 95,635,610	K1354E	possibly damaging	Het
Kcnk12	C	A	17: 87,746,649	R195L	probably benign	Het
Kcnn2	A	T	18: 45,592,345	I303F	probably damaging	Het
Kcnt1	T	C	2: 25,908,110	F879S	probably damaging	Het
Kndc1	T	C	7: 139,895,217	F11L	probably benign	Het
Kpna7	A	G	5: 144,989,795	F449S	probably damaging	Het
Krt77	G	T	15: 101,865,453	N255K	probably benign	Het
Loxhd1	T	C	18: 77,402,515	V1318A	probably damaging	Het
March10	A	T	11: 105,402,146	V145D	possibly damaging	Het
Mcpt1	T	A	14: 56,019,512	M169K	probably benign	Het
Mdc1	T	A	17: 35,847,820	V364E	probably benign	Het
Mfsd11	T	C	11: 116,871,384	F270S	probably damaging	Het
Mfsd4b2	T	G	10: 39,922,035	D108A	probably benign	Het
Mink1	A	T	11: 70,610,059		probably benign	Het
Mmp25	T	C	17: 23,631,074	Y504C	probably damaging	Het
Ms4a13	C	T	19: 11,191,506	V52I	probably benign	Het
Msh4	C	T	3: 153,867,723		probably null	Het
Muc5b	T	G	7: 141,858,421	S1701R	unknown	Het
Naalad2	A	T	9: 18,330,641	S656T	probably benign	Het
Ncapd2	T	C	6: 125,187,089	Y64C	probably damaging	Het
Ncapg2	T	A	12: 116,425,800	S347T	possibly damaging	Het
Nipal4	T	C	11: 46,151,339	T172A	probably damaging	Het
Nrros	T	C	16: 32,143,087	K652R	probably benign	Het
Nrxn3	G	T	12: 89,512,085	A983S	possibly damaging	Het
Olfr1084	A	C	2: 86,639,144	L188R	probably damaging	Het
Olfr1187-ps1	T	C	2: 88,540,244		noncoding transcript	Het
Olfr1220	T	A	2: 89,097,925	M1L	probably damaging	Het
Olfr1249	T	A	2: 89,630,799	Y33F	probably damaging	Het
Olfr1283	T	C	2: 111,368,743	M37T	probably benign	Het
Olfr631	A	G	7: 103,929,032	T70A	possibly damaging	Het
Olfr938	A	T	9: 39,077,967	Y259*	probably null	Het
P2rx4	T	A	5: 122,719,165	S155T	probably benign	Het
P2rx4	T	G	5: 122,727,208	Y299D	probably damaging	Het
Pcsk6	A	T	7: 66,043,624	L7F	probably null	Het
Pdss2	T	C	10: 43,221,797		silent	Het
Pfkl	A	G	10: 77,991,370	V494A	possibly damaging	Het
Prep	G	T	10: 45,067,364	D12Y	possibly damaging	Het
Prg4	A	G	1: 150,452,350	F188S	probably damaging	Het
Ripor3	T	C	2: 167,997,287	Y98C	probably damaging	Het
Rnf216	T	A	5: 143,068,314		probably null	Het
Rnf24	A	G	2: 131,322,245		probably benign	Het
Scn3a	A	G	2: 65,497,398	M916T	probably benign	Het
Scnm1	T	C	3: 95,130,285	I157V	probably benign	Het
Sh2b3	C	G	5: 121,829,021	R10P	possibly damaging	Het
Slc25a27	T	C	17: 43,649,694	D211G	probably damaging	Het
Slc36a4	A	T	9: 15,727,028	Y250F	probably damaging	Het
Slc4a1	T	A	11: 102,356,525	E448V	probably damaging	Het
Slit1	C	A	19: 41,743,296	C38F	probably damaging	Het
Spock3	T	A	8: 63,355,300	N410K	unknown	Het
Supt20	G	T	3: 54,712,207	W370L	probably benign	Het
Tas2r139	T	A	6: 42,141,496	N187K	probably damaging	Het
Tbc1d9b	G	A	11: 50,140,484	V111I	probably benign	Het
Thsd7b	T	A	1: 130,210,320	Y1578*	probably null	Het
Tln2	T	A	9: 67,229,403	I1267F	probably damaging	Het
Tnk2	G	A	16: 32,671,367	V363I	probably damaging	Het
Ttc32	A	G	12: 9,035,870	K139R	possibly damaging	Het
Vmn1r30	G	C	6: 58,435,565	T94S	possibly damaging	Het
Vmn1r90	G	A	7: 14,561,855	T106I	probably damaging	Het
Zfp677	T	A	17: 21,398,258	C526S	probably damaging	Het
Zfp831	T	G	2: 174,643,627	S32A	probably benign	Het

Other mutations in Lair1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00672:Lair1	APN	7	4028731	missense	probably benign	0.01
IGL01475:Lair1	APN	7	4009684	utr 3 prime	probably benign
IGL02696:Lair1	APN	7	4010849	intron	probably benign
IGL02749:Lair1	APN	7	4028901	missense	possibly damaging	0.50
R0396:Lair1	UTSW	7	4010786	missense	probably damaging	1.00
R0703:Lair1	UTSW	7	4010760	missense	probably null	0.99
R1053:Lair1	UTSW	7	4028785	missense	probably damaging	1.00
R1332:Lair1	UTSW	7	4010596	missense	possibly damaging	0.77
R1717:Lair1	UTSW	7	4010789	missense	probably damaging	1.00
R2022:Lair1	UTSW	7	4063064	splice site	probably null
R2509:Lair1	UTSW	7	4010783	missense	probably damaging	1.00
R3721:Lair1	UTSW	7	4010783	missense	probably damaging	1.00
R4021:Lair1	UTSW	7	4055916	critical splice donor site	probably null
R4784:Lair1	UTSW	7	4009732	missense	probably benign	0.15
R4873:Lair1	UTSW	7	4029034	missense	probably benign	0.05
R4875:Lair1	UTSW	7	4029034	missense	probably benign	0.05
R4940:Lair1	UTSW	7	4028949	missense	probably benign	0.00
R5125:Lair1	UTSW	7	4010489	missense	possibly damaging	0.92
R5178:Lair1	UTSW	7	4010489	missense	possibly damaging	0.92
R5965:Lair1	UTSW	7	4029024	missense	possibly damaging	0.46
R6119:Lair1	UTSW	7	4028896	missense	probably benign	0.43
R6265:Lair1	UTSW	7	4055827	intron	probably benign
R6305:Lair1	UTSW	7	4010728	critical splice donor site	probably null
R6915:Lair1	UTSW	7	4055953	missense	possibly damaging	0.89
R7964:Lair1	UTSW	7	4010804	missense	probably benign	0.22
R7991:Lair1	UTSW	7	4028970	missense	probably damaging	1.00
R9414:Lair1	UTSW	7	4010820	missense	probably benign	0.09
R9787:Lair1	UTSW	7	4010795	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TTTGGGAGTCCTGAGAATAGTCAG -3'
(R):5'- TCAGGCCAACACTTATGACC -3'

Sequencing Primer
(F):5'- GTCAGAATCAGTTCACATTTAGGAGG -3'
(R):5'- ACTTATGACCAGTGACACAAGG -3'

Posted On

2017-12-01