Mutagenetix > Incidental Mutation

Incidental Mutation 'R1985:Ly9'

220407

Institutional Source

Beutler Lab

Gene Symbol

Ly9

Ensembl Gene

ENSMUSG00000004707

Gene Name

lymphocyte antigen 9

Synonyms

T100, Lgp100, CD229, SLAMF3

MMRRC Submission

039997-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1985 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

171416172-171434917 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 171427341 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 405 (S405P)

Ref Sequence

ENSEMBL: ENSMUSP00000106908 (fasta)

Gene Model

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

AlphaFold

Q01965

Predicted Effect

probably damaging
Transcript: ENSMUST00000004827
AA Change: S295P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707
AA Change: S295P

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 damaging
Transcript: ENSMUST00000068878
AA Change: S405P

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

SMART Domains

Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: S405P

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 damaging
Transcript: ENSMUST00000111277
AA Change: S405P

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

SMART Domains

Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707
AA Change: S405P

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

Meta Mutation Damage Score

0.3773

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.8%
20x: 94.2%

Validation Efficiency

94% (76/81)

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abhd8	C	A	8: 71,916,157 (GRCm39)		probably benign	Het
Adam5	A	T	8: 25,236,755 (GRCm39)	D648E	probably benign	Het
Akr1d1	A	G	6: 37,535,336 (GRCm39)	D240G	probably damaging	Het
Ankmy2	A	G	12: 36,207,363 (GRCm39)	H3R	possibly damaging	Het
Anpep	A	C	7: 79,490,605 (GRCm39)		probably null	Het
Apobr	A	G	7: 126,186,903 (GRCm39)	T20A	possibly damaging	Het
Atp2a2	A	T	5: 122,604,899 (GRCm39)	Y427N	probably benign	Het
Camkk2	A	C	5: 122,902,190 (GRCm39)	S40A	possibly damaging	Het
Camp	T	C	9: 109,677,497 (GRCm39)	N112S	probably benign	Het
Cbx7	A	G	15: 79,802,591 (GRCm39)	S229P	probably damaging	Het
Cnot2	T	C	10: 116,363,781 (GRCm39)	N41S	probably damaging	Het
Dchs1	A	G	7: 105,421,605 (GRCm39)	F272L	possibly damaging	Het
Dct	T	C	14: 118,273,954 (GRCm39)	K318E	probably benign	Het
Dhrs11	A	C	11: 84,719,633 (GRCm39)	L31V	probably damaging	Het
Dnah7a	T	C	1: 53,543,093 (GRCm39)	D2359G	probably benign	Het
Dnajc7	A	G	11: 100,481,718 (GRCm39)	S305P	probably benign	Het
Dscc1	CTGAATGAAT	CTGAAT	15: 54,943,572 (GRCm39)		probably benign	Het
Flnc	A	G	6: 29,444,415 (GRCm39)		probably benign	Het
Garin3	T	C	11: 46,298,693 (GRCm39)	*666Q	probably null	Het
Gm7535	A	G	17: 18,131,800 (GRCm39)		probably benign	Het
Grtp1	A	G	8: 13,229,376 (GRCm39)	F313L	probably damaging	Het
Haus6	T	C	4: 86,511,846 (GRCm39)	Y425C	possibly damaging	Het
Hdac1	T	A	4: 129,422,753 (GRCm39)	N83Y	possibly damaging	Het
Hdlbp	A	G	1: 93,358,840 (GRCm39)	I237T	probably damaging	Het
Hfm1	A	T	5: 107,046,442 (GRCm39)	D481E	probably damaging	Het
Hipk3	T	C	2: 104,264,780 (GRCm39)	I737V	probably benign	Het
Il23r	T	A	6: 67,467,652 (GRCm39)		probably null	Het
Il24	G	A	1: 130,810,268 (GRCm39)	T196I	probably benign	Het
Ints3	C	T	3: 90,307,610 (GRCm39)		probably null	Het
Kcna6	T	C	6: 126,715,473 (GRCm39)	E472G	probably benign	Het
Kcnj16	C	T	11: 110,916,409 (GRCm39)	T357M	probably benign	Het
Kdm4b	T	A	17: 56,708,302 (GRCm39)	V957E	probably damaging	Het
Kif21b	G	A	1: 136,075,284 (GRCm39)	D166N	probably damaging	Het
Klhl11	G	T	11: 100,354,070 (GRCm39)	Q584K	probably benign	Het
Krt9	A	T	11: 100,080,817 (GRCm39)	M345K	probably benign	Het
Lgr5	T	C	10: 115,331,150 (GRCm39)		probably benign	Het
Lilrb4b	A	T	10: 51,357,831 (GRCm39)	Q80L	possibly damaging	Het
Lrrc69	T	C	4: 14,708,669 (GRCm39)	E225G	possibly damaging	Het
Myh2	A	G	11: 67,071,740 (GRCm39)	D519G	possibly damaging	Het
Nav3	G	A	10: 109,606,045 (GRCm39)		probably benign	Het
Nfkb1	G	A	3: 135,321,110 (GRCm39)	T215I	possibly damaging	Het
Ninj2	A	T	6: 120,175,600 (GRCm39)		probably benign	Het
Obsl1	A	G	1: 75,482,244 (GRCm39)	C209R	probably damaging	Het
Or13a25	G	A	7: 140,247,734 (GRCm39)	C171Y	probably damaging	Het
Or2d4	A	G	7: 106,544,133 (GRCm39)	I25T	probably benign	Het
Or2j6	A	T	7: 139,980,713 (GRCm39)	M82K	possibly damaging	Het
Or2t44	A	C	11: 58,677,210 (GRCm39)	D50A	probably damaging	Het
Or2y1g	T	C	11: 49,171,110 (GRCm39)	I45T	probably damaging	Het
Or52z14	A	T	7: 103,252,879 (GRCm39)	Y6F	probably benign	Het
Otud4	G	C	8: 80,366,641 (GRCm39)	R36P	probably damaging	Het
Pcnt	C	T	10: 76,216,171 (GRCm39)	R2239H	possibly damaging	Het
Pgbd5	T	A	8: 125,097,331 (GRCm39)	M491L	probably benign	Het
Pitrm1	A	T	13: 6,608,220 (GRCm39)	D316V	probably damaging	Het
Plod3	A	G	5: 137,019,707 (GRCm39)		probably null	Het
Plppr3	A	T	10: 79,703,294 (GRCm39)	Y63*	probably null	Het
Pramel52-ps	A	T	5: 94,531,931 (GRCm39)	I272L	probably benign	Het
Prickle2	T	C	6: 92,388,433 (GRCm39)	D323G	probably damaging	Het
Psmd11	A	T	11: 80,336,089 (GRCm39)	I114F	probably damaging	Het
Ptch1	T	G	13: 63,672,773 (GRCm39)	E944A	probably benign	Het
Rbp3	C	T	14: 33,677,975 (GRCm39)	T641M	probably damaging	Het
Rbp3	T	G	14: 33,678,418 (GRCm39)	S789A	probably benign	Het
Rfxap	C	A	3: 54,714,747 (GRCm39)	R117L	probably damaging	Het
Rims2	T	A	15: 39,208,710 (GRCm39)	M171K	probably damaging	Het
Scin	A	G	12: 40,183,907 (GRCm39)		probably null	Het
Scn11a	A	G	9: 119,583,744 (GRCm39)	S1624P	probably benign	Het
Slc41a3	G	A	6: 90,619,210 (GRCm39)	V330M	probably damaging	Het
Slc9c1	A	G	16: 45,370,469 (GRCm39)	I237V	probably benign	Het
Spag6	A	G	2: 18,736,930 (GRCm39)	I218V	probably benign	Het
Stam2	T	C	2: 52,599,638 (GRCm39)	T257A	possibly damaging	Het
Tbc1d24	G	A	17: 24,426,938 (GRCm39)	R318*	probably null	Het
Tedc2	T	A	17: 24,435,291 (GRCm39)	E366V	probably damaging	Het
Tedc2	C	A	17: 24,435,292 (GRCm39)	E366*	probably null	Het
Trpm3	T	A	19: 22,903,446 (GRCm39)	Y1069N	possibly damaging	Het
Tuba8	A	G	6: 121,197,479 (GRCm39)	D47G	probably benign	Het
Tulp3	A	T	6: 128,303,769 (GRCm39)	S277T	probably benign	Het
Uqcc6	T	A	10: 82,456,051 (GRCm39)	T37S	possibly damaging	Het
Wdr7	GTT	GT	18: 63,893,654 (GRCm39)		probably null	Het
Ybx2	A	G	11: 69,827,294 (GRCm39)		probably null	Het
Zfp407	C	T	18: 84,577,898 (GRCm39)	A1072T	probably benign	Het
Zfp788	T	A	7: 41,299,905 (GRCm39)	I795N	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
R2219:Ly9	UTSW	1	171,425,249 (GRCm39)	splice site	probably null
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'- GTCTCTCACTGGCTTTTATAAACAGC -3'
(R):5'- TGACAGGTCTGGTTCCATGC -3'

Sequencing Primer
(F):5'- GACATCAAAGTCCCAGCTTCTATAG -3'
(R):5'- GTCTGGTTCCATGCTGGCTC -3'

Posted On

2014-08-25