Mutagenetix > Incidental Mutation

Incidental Mutation 'R8892:Ly9'

677728

Institutional Source

Beutler Lab

Gene Symbol

Ly9

Ensembl Gene

ENSMUSG00000004707

Gene Name

lymphocyte antigen 9

Synonyms

T100, Lgp100, CD229, SLAMF3

MMRRC Submission

068695-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8892 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

171416172-171434917 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 171421465 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 595 (D595E)

Ref Sequence

ENSEMBL: ENSMUSP00000069319 (fasta)

Gene Model

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

AlphaFold

Q01965

Predicted Effect

possibly damaging
Transcript: ENSMUST00000004827
AA Change: D485E

PolyPhen 2 Score 0.897 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707
AA Change: D485E

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

possibly damaging
Transcript: ENSMUST00000068878
AA Change: D595E

PolyPhen 2 Score 0.811 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: D595E

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

possibly damaging
Transcript: ENSMUST00000111277
AA Change: D595E

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707
AA Change: D595E

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: 100.0%
10x: 99.8%
20x: 99.6%

Validation Efficiency

100% (76/76)

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: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca14	T	A	7: 119,815,606 (GRCm39)	L285I	probably damaging	Het
Abcc2	T	G	19: 43,795,571 (GRCm39)	S442R	possibly damaging	Het
Adgrl3	A	T	5: 81,874,516 (GRCm39)	I938F	probably damaging	Het
Adpgk	A	G	9: 59,217,623 (GRCm39)	Y212C	probably damaging	Het
Ahcyl1	C	T	3: 107,579,378 (GRCm39)	D219N	probably benign	Het
Ap3b1	G	A	13: 94,679,348 (GRCm39)	V997M	unknown	Het
Bbs1	A	C	19: 4,942,954 (GRCm39)	S479A	probably benign	Het
Bean1	A	T	8: 104,943,610 (GRCm39)	D231V	probably damaging	Het
Cacnb1	A	T	11: 97,901,192 (GRCm39)	V220E	probably damaging	Het
Camkv	C	T	9: 107,823,333 (GRCm39)	R120*	probably null	Het
Ccny	T	G	18: 9,345,235 (GRCm39)	S180R	probably damaging	Het
Cdh23	G	T	10: 60,143,284 (GRCm39)	H3012Q	probably damaging	Het
Chd9	A	G	8: 91,660,468 (GRCm39)	N476S	unknown	Het
Clasp2	T	A	9: 113,709,251 (GRCm39)	L680Q	probably damaging	Het
Clip1	A	T	5: 123,717,565 (GRCm39)	S1241R	probably benign	Het
Cramp1	C	T	17: 25,202,114 (GRCm39)	G456D	probably damaging	Het
Csmd3	T	A	15: 47,604,634 (GRCm39)	K1036N		Het
Ctnna1	G	A	18: 35,372,586 (GRCm39)	V514I	possibly damaging	Het
Ddr1	A	C	17: 35,993,556 (GRCm39)	I852S	probably benign	Het
Dhrs1	G	A	14: 55,977,404 (GRCm39)	A238V	possibly damaging	Het
Echs1	A	C	7: 139,688,031 (GRCm39)	L258R	probably damaging	Het
Epha8	G	T	4: 136,661,850 (GRCm39)	H582N	probably benign	Het
Fhod3	G	A	18: 25,189,452 (GRCm39)		probably null	Het
Gm40460	ACCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAG	ACCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAGGAACTACAGCCTCCCTTGCAGCCCCCACAG	7: 141,794,450 (GRCm39)		probably benign	Het
Gpr179	T	C	11: 97,226,590 (GRCm39)	D1855G	possibly damaging	Het
Idh2	TCCCAGG	T	7: 79,748,079 (GRCm39)		probably benign	Het
Ipo9	T	C	1: 135,314,544 (GRCm39)	N904S	possibly damaging	Het
Itih3	A	G	14: 30,637,635 (GRCm39)	V508A	probably benign	Het
Klhl14	T	G	18: 21,691,220 (GRCm39)	T437P	possibly damaging	Het
Krt5	T	C	15: 101,619,185 (GRCm39)	M268V	probably benign	Het
Lama4	T	A	10: 38,973,194 (GRCm39)	L1587Q	probably damaging	Het
Lhx4	T	C	1: 155,581,013 (GRCm39)	T171A	possibly damaging	Het
Lrfn2	A	C	17: 49,377,376 (GRCm39)	E152D	probably damaging	Het
Ltn1	A	T	16: 87,229,230 (GRCm39)		probably benign	Het
Macf1	A	G	4: 123,249,036 (GRCm39)	L7165P	probably damaging	Het
Magi3	C	T	3: 103,958,141 (GRCm39)	G648D	probably damaging	Het
Mgll	T	A	6: 88,743,306 (GRCm39)	C109S	unknown	Het
Micall2	T	A	5: 139,703,254 (GRCm39)	H194L	probably damaging	Het
Mindy4	T	C	6: 55,255,223 (GRCm39)	L567P	probably benign	Het
Mmp16	T	A	4: 18,051,820 (GRCm39)	Y270N	probably damaging	Het
Naa16	A	T	14: 79,628,016 (GRCm39)	F14I	probably benign	Het
Nme6	T	G	9: 109,668,706 (GRCm39)	F41V	probably damaging	Het
Npffr1	A	G	10: 61,449,939 (GRCm39)	N71S	possibly damaging	Het
Or1b1	C	A	2: 36,995,523 (GRCm39)	L46F	probably damaging	Het
Or1p4-ps1	T	C	11: 74,207,949 (GRCm39)	W33R	probably damaging	Het
Or4k41	A	G	2: 111,279,967 (GRCm39)	I161V	probably benign	Het
Pard3b	T	A	1: 62,677,026 (GRCm39)	Y1186N	probably damaging	Het
Pou2f1	A	T	1: 165,708,027 (GRCm39)	S552T	unknown	Het
Ppp2r3c	A	T	12: 55,336,453 (GRCm39)	L233Q	possibly damaging	Het
Prl8a1	G	A	13: 27,766,069 (GRCm39)	H9Y	possibly damaging	Het
Rnf135	C	T	11: 80,074,957 (GRCm39)	T72I	probably benign	Het
Rsf1	A	T	7: 97,328,171 (GRCm39)	I1058F		Het
Slc39a6	A	T	18: 24,729,386 (GRCm39)	Y442*	probably null	Het
Slc44a2	G	A	9: 21,253,153 (GRCm39)		probably benign	Het
Slc4a11	T	G	2: 130,529,140 (GRCm39)	S437R	probably damaging	Het
Spc24	G	A	9: 21,668,994 (GRCm39)	Q98*	probably null	Het
Spock3	T	A	8: 63,404,986 (GRCm39)	Y51*	probably null	Het
Sptbn1	A	G	11: 30,067,800 (GRCm39)	Y1805H	probably benign	Het
Tango6	A	G	8: 107,468,845 (GRCm39)	I780M	probably benign	Het
Tcerg1l	C	T	7: 137,999,260 (GRCm39)	W41*	probably null	Het
Tdrd9	A	G	12: 111,979,718 (GRCm39)	Y401C	probably benign	Het
Tex47	A	T	5: 7,355,115 (GRCm39)	I99F	probably damaging	Het
Tlr9	G	A	9: 106,099,834 (GRCm39)		probably benign	Het
Tmem209	T	A	6: 30,497,942 (GRCm39)	S276C	possibly damaging	Het
Tmprss11f	A	C	5: 86,687,618 (GRCm39)	S97A	possibly damaging	Het
Top6bl	A	G	19: 4,699,721 (GRCm39)	V494A	possibly damaging	Het
Ttc7	T	A	17: 87,637,520 (GRCm39)	M425K	probably damaging	Het
Ttn	C	T	2: 76,739,466 (GRCm39)	G3737D	unknown	Het
Tyk2	T	C	9: 21,027,463 (GRCm39)	H503R	probably benign	Het
Unc13b	A	T	4: 43,176,484 (GRCm39)	R2437S	unknown	Het
Uqcrc1	C	T	9: 108,766,186 (GRCm39)	R58C	probably damaging	Het
Vmn1r160	G	A	7: 22,571,474 (GRCm39)	V276I	probably benign	Het
Vmn2r112	A	G	17: 22,837,612 (GRCm39)	Y691C	probably damaging	Het
Vmn2r87	A	C	10: 130,308,105 (GRCm39)	I711S	probably damaging	Het
Vmn2r94	A	G	17: 18,464,335 (GRCm39)	S652P	possibly damaging	Het
Vps50	T	A	6: 3,536,967 (GRCm39)	C313S	probably damaging	Het
Xrcc5	T	G	1: 72,382,190 (GRCm39)	D455E	possibly damaging	Het
Zdhhc6	T	A	19: 55,290,987 (GRCm39)		probably benign	Het
Zfp964	G	A	8: 70,116,405 (GRCm39)	G335D	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
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
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'- CTGAACTGTATGGCATCAGTCTG -3'
(R):5'- TGCTAAGACCACCAGGCATC -3'

Sequencing Primer
(F):5'- GCATCAGTCTGTATGGTCCTTGAC -3'
(R):5'- TCTGAGAGCAGCGCAAC -3'

Posted On

2021-08-02