Mutagenetix > Incidental Mutation

Incidental Mutation 'R2219:Ly9'

241303

Institutional Source

Beutler Lab

Gene Symbol

Ly9

Ensembl Gene

ENSMUSG00000004707

Gene Name

lymphocyte antigen 9

Synonyms

T100, Lgp100, CD229, SLAMF3

MMRRC Submission

040221-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2219 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

171416172-171434917 bp(-) (GRCm39)

Type of Mutation

splice site (3 bp from exon)

DNA Base Change (assembly)

T to C at 171425249 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000106908 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000004827] [ENSMUST00000068878] [ENSMUST00000111277] [ENSMUST00000111277] [ENSMUST00000143463] [ENSMUST00000194797]

AlphaFold

Q01965

Predicted Effect

probably null
Transcript: ENSMUST00000004827

SMART Domains

Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707

Domain	Start	End	E-Value	Type
Pfam:Ig_3	46	116	7.9e-9	PFAM
Pfam:Ig_2	46	129	5.4e-10	PFAM
IG	143	246	1.49e-2	SMART
Pfam:Ig_3	251	320	4.1e-13	PFAM
Pfam:Ig_2	251	330	7.5e-6	PFAM
transmembrane domain	345	364	N/A	INTRINSIC
low complexity region	420	436	N/A	INTRINSIC
low complexity region	519	530	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000068878

SMART Domains

Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707

Domain	Start	End	E-Value	Type
IG	52	151	8.72e-4	SMART
Pfam:Ig_3	156	226	5.6e-8	PFAM
Pfam:Ig_2	156	239	4e-8	PFAM
IG	253	356	1.49e-2	SMART
Pfam:Ig_3	361	430	5.4e-10	PFAM
low complexity region	433	441	N/A	INTRINSIC
transmembrane domain	455	474	N/A	INTRINSIC
low complexity region	530	546	N/A	INTRINSIC
low complexity region	629	640	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000111277

SMART Domains

Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707

Domain	Start	End	E-Value	Type
IG	52	151	8.72e-4	SMART
Pfam:Ig_3	156	226	9.9e-9	PFAM
Pfam:Ig_2	156	239	6.8e-10	PFAM
IG	253	356	1.49e-2	SMART
Pfam:Ig_3	361	430	5e-13	PFAM
Pfam:Ig_2	361	440	9.4e-6	PFAM
transmembrane domain	455	474	N/A	INTRINSIC
low complexity region	530	546	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000111277

SMART Domains

Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707

Domain	Start	End	E-Value	Type
IG	52	151	8.72e-4	SMART
Pfam:Ig_3	156	226	9.9e-9	PFAM
Pfam:Ig_2	156	239	6.8e-10	PFAM
IG	253	356	1.49e-2	SMART
Pfam:Ig_3	361	430	5e-13	PFAM
Pfam:Ig_2	361	440	9.4e-6	PFAM
transmembrane domain	455	474	N/A	INTRINSIC
low complexity region	530	546	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000143463

SMART Domains

Protein: ENSMUSP00000137924
Gene: ENSMUSG00000004707

Domain	Start	End	E-Value	Type
transmembrane domain	28	50	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146596

Predicted Effect

probably benign
Transcript: ENSMUST00000194797

SMART Domains

Protein: ENSMUSP00000141898
Gene: ENSMUSG00000004709

Domain	Start	End	E-Value	Type
IG	26	128	4.23e-2	SMART
Pfam:Ig_2	134	221	6.5e-5	PFAM
transmembrane domain	226	248	N/A	INTRINSIC

Coding Region Coverage

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

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] LY9 belongs to the SLAM family of immunomodulatory receptors (see SLAMF1; MIM 603492) and interacts with the adaptor molecule SAP (SH2D1A; MIM 300490) (Graham et al., 2006 [PubMed 16365421]).[supplied by OMIM, Mar 2008]
PHENOTYPE: This locus controls an antigen on thymocytes, lymphocytes and bone marrow cells. The a allele determines Ly9.1 antigen in A/J, 129/Re, BALB/c and C3H/He; the b allele determines antigen Ly9.2 in the C57 family of strains, HTI/Go, MA/My, F/St and C58/Lw. Null mutants are viable, healthy and fertile. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933421I07Rik	A	G	7: 42,095,769 (GRCm39)	Y160H	probably damaging	Het
Adamts16	G	A	13: 70,927,637 (GRCm39)		probably benign	Het
Adgre1	T	A	17: 57,708,912 (GRCm39)	N34K	possibly damaging	Het
Ago2	T	A	15: 73,018,260 (GRCm39)	E59D	probably benign	Het
Akap8l	G	T	17: 32,553,605 (GRCm39)	Q372K	probably benign	Het
Aox1	A	G	1: 58,388,289 (GRCm39)		probably null	Het
Apc2	T	C	10: 80,144,943 (GRCm39)	V618A	probably benign	Het
Cacna1d	A	T	14: 29,764,047 (GRCm39)	C2140S	probably damaging	Het
Cadps2	A	G	6: 23,410,831 (GRCm39)	L671P	probably damaging	Het
Capn9	C	T	8: 125,335,898 (GRCm39)	R529*	probably null	Het
Ccdc180	T	A	4: 45,944,949 (GRCm39)	N1452K	probably damaging	Het
Cdh5	A	T	8: 104,869,538 (GRCm39)	I755F	possibly damaging	Het
Cdkal1	T	A	13: 29,538,741 (GRCm39)	M473L	probably benign	Het
Cfap65	T	C	1: 74,943,184 (GRCm39)	I1614V	probably damaging	Het
Champ1	A	G	8: 13,930,017 (GRCm39)	H725R	probably damaging	Het
Cntnap5a	A	T	1: 116,508,369 (GRCm39)	T1294S	possibly damaging	Het
Cops8	A	C	1: 90,534,341 (GRCm39)	N94T	probably benign	Het
Cpne7	G	T	8: 123,851,177 (GRCm39)	V155L	probably benign	Het
Dhx29	T	C	13: 113,089,338 (GRCm39)	V703A	probably damaging	Het
Dhx30	A	G	9: 109,916,703 (GRCm39)	L575P	probably damaging	Het
Dmc1	T	A	15: 79,469,327 (GRCm39)	H156L	possibly damaging	Het
Dnmt3a	A	G	12: 3,899,654 (GRCm39)		probably benign	Het
Dst	C	G	1: 34,209,514 (GRCm39)	L869V	probably damaging	Het
Eif3d	A	T	15: 77,849,142 (GRCm39)	M180K	probably benign	Het
Erbb3	T	C	10: 128,405,740 (GRCm39)	T1173A	probably damaging	Het
Fat4	A	T	3: 39,064,364 (GRCm39)	K4773N	probably damaging	Het
Fbn2	G	A	18: 58,186,035 (GRCm39)	P1771L	possibly damaging	Het
Fer1l4	T	G	2: 155,873,684 (GRCm39)	Y1207S	probably damaging	Het
Fermt2	G	A	14: 45,713,354 (GRCm39)	T87I	probably benign	Het
Fpr3	T	A	17: 18,191,644 (GRCm39)	M305K	possibly damaging	Het
Fzd2	A	G	11: 102,496,249 (GRCm39)	E231G	probably benign	Het
Ggcx	T	C	6: 72,404,965 (GRCm39)	Y458H	probably benign	Het
Ggt7	A	G	2: 155,337,639 (GRCm39)	S504P	probably damaging	Het
Gm4884	A	G	7: 40,692,910 (GRCm39)	H293R	possibly damaging	Het
Gm5475	A	G	15: 100,322,094 (GRCm39)		probably benign	Het
Gm5930	A	T	14: 44,573,993 (GRCm39)	L115M	probably damaging	Het
Itln1	T	A	1: 171,359,115 (GRCm39)	T122S	probably damaging	Het
Itpr3	T	A	17: 27,334,027 (GRCm39)	L2033Q	probably benign	Het
Lama2	T	C	10: 26,919,565 (GRCm39)	D2222G	probably damaging	Het
Lars2	T	C	9: 123,247,845 (GRCm39)	L334P	probably damaging	Het
Man1a	T	C	10: 53,853,145 (GRCm39)	I324M	probably damaging	Het
Mast3	T	C	8: 71,233,607 (GRCm39)	E994G	probably damaging	Het
Mettl21a	A	T	1: 64,655,442 (GRCm39)	V46E	probably damaging	Het
Mmp15	A	G	8: 96,096,801 (GRCm39)	D398G	probably benign	Het
Mybpc1	T	A	10: 88,391,540 (GRCm39)	D319V	probably damaging	Het
Or10ad1c	T	A	15: 98,084,848 (GRCm39)	K277*	probably null	Het
Or4a47	A	T	2: 89,665,769 (GRCm39)	D173E	probably damaging	Het
Or4a78	A	T	2: 89,498,211 (GRCm39)	N6K	possibly damaging	Het
Or4c35	G	A	2: 89,808,256 (GRCm39)	V45I	possibly damaging	Het
Or4f61	A	T	2: 111,922,752 (GRCm39)	I98N	probably damaging	Het
Or5b113	T	A	19: 13,342,901 (GRCm39)	I303N	possibly damaging	Het
Or5p5	G	A	7: 107,414,429 (GRCm39)	V213I	probably benign	Het
Or9m1	A	C	2: 87,733,269 (GRCm39)	Y250*	probably null	Het
Otogl	C	T	10: 107,692,838 (GRCm39)	C882Y	probably damaging	Het
Parp10	A	G	15: 76,117,783 (GRCm39)	Y868H	probably damaging	Het
Pick1	T	A	15: 79,123,899 (GRCm39)	I90N	probably damaging	Het
Piezo1	C	T	8: 123,218,227 (GRCm39)	V1170I	probably benign	Het
Pim3	G	A	15: 88,747,115 (GRCm39)	V54I	possibly damaging	Het
Pinlyp	T	C	7: 24,245,433 (GRCm39)		probably benign	Het
Pira12	A	T	7: 3,900,488 (GRCm39)	N87K	probably benign	Het
Ppfia3	G	A	7: 45,004,314 (GRCm39)	Q473*	probably null	Het
Rab3gap2	G	A	1: 185,008,113 (GRCm39)	G1056E	probably damaging	Het
Ralgapa2	G	A	2: 146,263,599 (GRCm39)	T706I	probably benign	Het
Reln	T	C	5: 22,177,045 (GRCm39)	T1874A	possibly damaging	Het
Rftn1	C	A	17: 50,476,173 (GRCm39)	M1I	probably null	Het
Ros1	T	A	10: 52,042,175 (GRCm39)	Q250L	probably damaging	Het
Slc11a1	T	A	1: 74,419,824 (GRCm39)	F166I	probably damaging	Het
Slc17a9	A	G	2: 180,373,755 (GRCm39)	T59A	probably benign	Het
Slc26a5	T	C	5: 22,028,476 (GRCm39)	K364R	probably damaging	Het
Slitrk2	T	C	X: 65,698,754 (GRCm39)	I415T	probably damaging	Het
Stom	A	G	2: 35,211,613 (GRCm39)	I136T	possibly damaging	Het
Strc	G	T	2: 121,195,004 (GRCm39)	P1728T	probably damaging	Het
Telo2	C	A	17: 25,322,673 (GRCm39)	V640F	probably benign	Het
Tg	T	C	15: 66,553,782 (GRCm39)	V399A	probably benign	Het
Tmem214	A	G	5: 31,030,975 (GRCm39)	K383E	possibly damaging	Het
Tomm40l	A	T	1: 171,049,550 (GRCm39)	L13*	probably null	Het
Tonsl	A	T	15: 76,518,840 (GRCm39)	N526K	probably damaging	Het
Top2b	T	G	14: 16,409,189 (GRCm38)	I777M	probably damaging	Het
Tymp	T	A	15: 89,258,965 (GRCm39)	M240L	probably benign	Het
Ubr2	A	T	17: 47,296,968 (GRCm39)	S271T	possibly damaging	Het
Uggt2	A	T	14: 119,312,749 (GRCm39)	N353K	probably damaging	Het
Ugt2b35	T	A	5: 87,151,191 (GRCm39)	F266I	possibly damaging	Het
Vmn2r103	C	T	17: 20,013,909 (GRCm39)	R234W	probably damaging	Het
Zfp109	C	A	7: 23,927,886 (GRCm39)	D508Y	probably damaging	Het
Zfp623	T	C	15: 75,819,379 (GRCm39)	S112P	possibly damaging	Het
Zfp735	A	G	11: 73,601,851 (GRCm39)	N265S	possibly damaging	Het
Zfp879	A	G	11: 50,724,094 (GRCm39)	C321R	probably damaging	Het

Other mutations in Ly9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00090:Ly9	APN	1	171,421,019 (GRCm39)	missense	probably damaging	1.00
IGL00640:Ly9	APN	1	171,429,447 (GRCm39)	missense	possibly damaging	0.65
IGL01899:Ly9	APN	1	171,434,815 (GRCm39)	missense	probably damaging	0.99
IGL02714:Ly9	APN	1	171,432,686 (GRCm39)	missense	possibly damaging	0.60
IGL03086:Ly9	APN	1	171,432,738 (GRCm39)	missense	probably benign	0.01
R0647:Ly9	UTSW	1	171,427,376 (GRCm39)	missense	probably damaging	1.00
R1292:Ly9	UTSW	1	171,416,671 (GRCm39)	splice site	probably null
R1422:Ly9	UTSW	1	171,428,780 (GRCm39)	missense	probably damaging	1.00
R1598:Ly9	UTSW	1	171,424,075 (GRCm39)	missense	probably benign	0.03
R1985:Ly9	UTSW	1	171,427,341 (GRCm39)	missense	probably damaging	1.00
R2427:Ly9	UTSW	1	171,434,800 (GRCm39)	missense	probably damaging	0.99
R3764:Ly9	UTSW	1	171,421,712 (GRCm39)	missense	possibly damaging	0.92
R3815:Ly9	UTSW	1	171,416,653 (GRCm39)	missense	possibly damaging	0.95
R3816:Ly9	UTSW	1	171,416,653 (GRCm39)	missense	possibly damaging	0.95
R3817:Ly9	UTSW	1	171,416,653 (GRCm39)	missense	possibly damaging	0.95
R3819:Ly9	UTSW	1	171,416,653 (GRCm39)	missense	possibly damaging	0.95
R4590:Ly9	UTSW	1	171,421,443 (GRCm39)	nonsense	probably null
R4653:Ly9	UTSW	1	171,421,597 (GRCm39)	missense	probably benign	0.41
R4755:Ly9	UTSW	1	171,434,806 (GRCm39)	missense	probably damaging	0.99
R4871:Ly9	UTSW	1	171,434,898 (GRCm39)	intron	probably benign
R5167:Ly9	UTSW	1	171,432,773 (GRCm39)	missense	probably damaging	1.00
R5203:Ly9	UTSW	1	171,427,347 (GRCm39)	missense	probably damaging	1.00
R5270:Ly9	UTSW	1	171,428,730 (GRCm39)	missense	probably damaging	0.99
R5692:Ly9	UTSW	1	171,432,755 (GRCm39)	frame shift	probably null
R5996:Ly9	UTSW	1	171,429,396 (GRCm39)	missense	probably damaging	1.00
R6389:Ly9	UTSW	1	171,424,105 (GRCm39)	missense	probably damaging	1.00
R6391:Ly9	UTSW	1	171,428,576 (GRCm39)	missense	possibly damaging	0.76
R6457:Ly9	UTSW	1	171,416,663 (GRCm39)	missense	probably damaging	1.00
R6730:Ly9	UTSW	1	171,432,737 (GRCm39)	missense	probably benign	0.14
R6732:Ly9	UTSW	1	171,421,653 (GRCm39)	missense	possibly damaging	0.74
R6862:Ly9	UTSW	1	171,428,723 (GRCm39)	missense	probably benign	0.21
R6866:Ly9	UTSW	1	171,432,847 (GRCm39)	missense	probably damaging	0.99
R7455:Ly9	UTSW	1	171,421,507 (GRCm39)	nonsense	probably null
R8105:Ly9	UTSW	1	171,432,890 (GRCm39)	splice site	probably null
R8349:Ly9	UTSW	1	171,421,586 (GRCm39)	missense	probably damaging	0.99
R8449:Ly9	UTSW	1	171,421,586 (GRCm39)	missense	probably damaging	0.99
R8836:Ly9	UTSW	1	171,432,559 (GRCm39)	nonsense	probably null
R8838:Ly9	UTSW	1	171,421,569 (GRCm39)	missense	probably damaging	1.00
R8856:Ly9	UTSW	1	171,432,587 (GRCm39)	missense	probably benign	0.03
R8892:Ly9	UTSW	1	171,421,465 (GRCm39)	missense	possibly damaging	0.81
R9414:Ly9	UTSW	1	171,427,275 (GRCm39)	missense	probably damaging	0.99
R9713:Ly9	UTSW	1	171,428,756 (GRCm39)	missense	probably damaging	1.00
R9748:Ly9	UTSW	1	171,428,722 (GRCm39)	missense	possibly damaging	0.65
X0062:Ly9	UTSW	1	171,432,789 (GRCm39)	missense	possibly damaging	0.82
Z1176:Ly9	UTSW	1	171,421,628 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGTCCATTAAGGCCACTGGG -3'
(R):5'- CCAATTAGGATGGTCACTGTGTTC -3'

Sequencing Primer
(F):5'- CAAGTGCACACGTGATGTCTGTAC -3'
(R):5'- GGTCACTGTGTTCTGTCAGTCATTC -3'

Posted On

2014-10-15