Mutagenetix > Incidental Mutation

Incidental Mutation 'R8856:Ly9'

675294

Institutional Source

Beutler Lab

Gene Symbol

Ly9

Ensembl Gene

ENSMUSG00000004707

Gene Name

lymphocyte antigen 9

Synonyms

T100, Lgp100, CD229, SLAMF3

MMRRC Submission

068737-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8856 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

171416172-171434917 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 171432587 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 142 (T142I)

Ref Sequence

ENSEMBL: ENSMUSP00000069319 (fasta)

Gene Model

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

AlphaFold

Q01965

Predicted Effect

probably benign
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 benign
Transcript: ENSMUST00000068878
AA Change: T142I

PolyPhen 2 Score 0.028 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: T142I

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

SMART Domains

Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707
AA Change: T142I

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

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: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

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: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2m	G	A	6: 121,618,349 (GRCm39)	R214H	probably benign	Het
Abca4	A	G	3: 121,906,096 (GRCm39)	S822G	probably benign	Het
Adgrv1	T	A	13: 81,707,621 (GRCm39)	I1262F	probably benign	Het
Agbl2	A	G	2: 90,632,088 (GRCm39)	D482G	probably damaging	Het
Asph	T	A	4: 9,630,947 (GRCm39)	T134S	possibly damaging	Het
Cacna1a	C	T	8: 85,286,070 (GRCm39)	A905V	probably benign	Het
Cacna1b	C	T	2: 24,569,530 (GRCm39)	R798H	probably benign	Het
Cpne8	G	T	15: 90,486,044 (GRCm39)	Q140K	probably benign	Het
Crocc2	A	T	1: 93,120,847 (GRCm39)	N538I	probably benign	Het
Cyp2j9	T	A	4: 96,462,184 (GRCm39)	I366F	probably damaging	Het
Dchs1	A	T	7: 105,410,064 (GRCm39)	D1769E	probably damaging	Het
Def6	A	T	17: 28,435,972 (GRCm39)	I44F	probably damaging	Het
Dnah7a	G	A	1: 53,462,422 (GRCm39)	T3723M	probably damaging	Het
Ecd	T	A	14: 20,387,140 (GRCm39)	Y198F	probably damaging	Het
Ecel1	A	C	1: 87,079,760 (GRCm39)	M451R	probably damaging	Het
Eea1	A	G	10: 95,831,506 (GRCm39)	D199G	probably benign	Het
Efna5	A	T	17: 62,914,374 (GRCm39)	I217N	unknown	Het
F13a1	A	T	13: 37,100,859 (GRCm39)	D428E	probably damaging	Het
Fads1	T	G	19: 10,170,276 (GRCm39)	I272S	probably benign	Het
Fam149a	C	T	8: 45,834,611 (GRCm39)	A63T		Het
Fam83a	A	T	15: 57,872,977 (GRCm39)	N269Y	probably damaging	Het
Fasn	G	A	11: 120,708,979 (GRCm39)	T568I	possibly damaging	Het
Fbn1	A	G	2: 125,156,637 (GRCm39)	S2363P	probably damaging	Het
Fbxl4	T	A	4: 22,390,803 (GRCm39)	W329R	probably damaging	Het
Fgf12	A	T	16: 28,008,233 (GRCm39)	V189E	probably damaging	Het
Frmd4b	A	T	6: 97,269,359 (GRCm39)	Y984*	probably null	Het
Galm	A	G	17: 80,490,661 (GRCm39)	T273A	possibly damaging	Het
Gm43302	A	G	5: 105,438,739 (GRCm39)	S50P	probably damaging	Het
Gm45861	C	T	8: 28,010,788 (GRCm39)	S561L	unknown	Het
Gnao1	A	G	8: 94,538,045 (GRCm39)	I28V	probably benign	Het
Golga4	A	G	9: 118,385,779 (GRCm39)	N967S	probably damaging	Het
Gpr155	A	T	2: 73,203,993 (GRCm39)	F274I	probably benign	Het
Grm1	A	C	10: 10,595,092 (GRCm39)	N845K	probably damaging	Het
Hnrnpa2b1	A	T	6: 51,443,120 (GRCm39)		probably null	Het
Hsf4	G	T	8: 105,996,628 (GRCm39)	D18Y	probably null	Het
Htt	T	A	5: 35,060,675 (GRCm39)	D2774E	probably benign	Het
Iars2	A	G	1: 185,028,621 (GRCm39)	I679T	probably benign	Het
Irf4	T	C	13: 30,945,414 (GRCm39)	F387L	probably damaging	Het
Itgb5	A	G	16: 33,720,962 (GRCm39)	Y342C	probably damaging	Het
Kcnmb4	A	G	10: 116,282,299 (GRCm39)	W133R	possibly damaging	Het
Ldhc	A	T	7: 46,525,999 (GRCm39)	H271L	probably benign	Het
Lmtk2	C	A	5: 144,113,079 (GRCm39)	D1266E	probably damaging	Het
Lrrtm1	C	A	6: 77,221,807 (GRCm39)	N421K	possibly damaging	Het
Manba	A	G	3: 135,223,764 (GRCm39)	Y217C	probably damaging	Het
Mapkbp1	T	C	2: 119,845,109 (GRCm39)	L330P	probably damaging	Het
Marchf2	A	T	17: 33,915,165 (GRCm39)	V143E	probably benign	Het
Mmel1	A	T	4: 154,969,478 (GRCm39)	D191V	possibly damaging	Het
Mrgpra1	A	T	7: 46,985,583 (GRCm39)	I32N	probably benign	Het
Mroh2b	C	T	15: 4,960,510 (GRCm39)	Q748*	probably null	Het
Mrpl34	T	G	8: 71,918,024 (GRCm39)	W66G	probably damaging	Het
Muc21	T	C	17: 35,931,865 (GRCm39)	T774A	unknown	Het
Nde1	T	A	16: 14,001,446 (GRCm39)	S165T		Het
Nek10	T	G	14: 14,937,610 (GRCm38)	I776M	probably damaging	Het
Nell2	A	G	15: 95,281,552 (GRCm39)	S385P	probably damaging	Het
Nsf	A	T	11: 103,821,568 (GRCm39)	F29Y	possibly damaging	Het
Nsmaf	A	T	4: 6,433,320 (GRCm39)	Y133*	probably null	Het
Ogfr	GGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGG	GGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGG	2: 180,237,059 (GRCm39)		probably benign	Het
Or14j8	A	T	17: 38,263,091 (GRCm39)	S275T	possibly damaging	Het
Pcdhb8	A	G	18: 37,489,776 (GRCm39)	I485V	probably benign	Het
Poteg	T	A	8: 27,938,033 (GRCm39)	M1K	probably null	Het
Pramel24	A	T	4: 143,453,303 (GRCm39)	N137I	probably benign	Het
Prdm5	G	A	6: 65,860,569 (GRCm39)	V418I	possibly damaging	Het
Psmc6	T	A	14: 45,578,320 (GRCm39)	C228S	probably damaging	Het
Ptgfrn	C	T	3: 100,963,927 (GRCm39)	A562T	possibly damaging	Het
Ralgapa2	G	T	2: 146,184,139 (GRCm39)	Q1576K	probably benign	Het
Ranbp9	C	T	13: 43,567,506 (GRCm39)	G400D	probably damaging	Het
Rgs11	A	T	17: 26,423,484 (GRCm39)	I134F	probably damaging	Het
Rnf150	T	A	8: 83,762,715 (GRCm39)	C317S	probably damaging	Het
Rrm2b	G	A	15: 37,960,858 (GRCm39)		probably benign	Het
Scai	T	C	2: 38,996,978 (GRCm39)	Q272R	probably benign	Het
Sec62	C	T	3: 30,847,506 (GRCm39)	R4C	possibly damaging	Het
Sgo2b	C	A	8: 64,393,091 (GRCm39)	L115F	probably null	Het
Slc44a3	G	A	3: 121,307,456 (GRCm39)	P177S	probably damaging	Het
Slc45a4	G	A	15: 73,457,966 (GRCm39)	L528F	probably damaging	Het
Slco1a1	G	T	6: 141,857,624 (GRCm39)	A569D	probably damaging	Het
Stam2	G	T	2: 52,604,984 (GRCm39)	Q184K	probably damaging	Het
Tada2b	A	T	5: 36,641,166 (GRCm39)	L79Q	probably damaging	Het
Tecpr1	T	C	5: 144,153,117 (GRCm39)	E204G	possibly damaging	Het
Tecta	A	T	9: 42,284,597 (GRCm39)	D829E	probably benign	Het
Tepsin	A	G	11: 119,982,654 (GRCm39)	V472A	probably benign	Het
Tnfrsf1a	G	A	6: 125,334,688 (GRCm39)	M109I	possibly damaging	Het
Trim42	A	T	9: 97,245,275 (GRCm39)	Y508*	probably null	Het
Trmo	T	G	4: 46,387,625 (GRCm39)	N65T	probably benign	Het
Tspear	G	T	10: 77,665,471 (GRCm39)	E86*	probably null	Het
Ubr1	A	T	2: 120,734,523 (GRCm39)	S1126T	probably damaging	Het
Usp50	C	A	2: 126,622,477 (GRCm39)	D28Y	probably damaging	Het
Utp6	T	A	11: 79,842,455 (GRCm39)	I225F	probably benign	Het
Utrn	T	C	10: 12,543,351 (GRCm39)	T1766A	probably benign	Het
Vcl	T	A	14: 21,045,160 (GRCm39)	N288K	probably benign	Het
Vmn2r69	T	C	7: 85,061,663 (GRCm39)	N104D	probably benign	Het
Zc3h7b	G	A	15: 81,656,681 (GRCm39)	R166Q	probably benign	Het
Zfhx4	T	A	3: 5,455,484 (GRCm39)	S1159R	probably benign	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
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
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'- CTATTGAGAAGAAGACACCAATGGC -3'
(R):5'- CCCCAAAGGCTCTTGCTTTAG -3'

Sequencing Primer
(F):5'- CTGACCCCAGTGATCTTGTGG -3'
(R):5'- CAAAGGCTCTTGCTTTAGTATTCTAC -3'

Posted On

2021-07-15