Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL00640:Ly9'

13595

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Ly9

Ensembl Gene

ENSMUSG00000004707

Gene Name

lymphocyte antigen 9

Synonyms

T100, Lgp100, CD229, SLAMF3

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

IGL00640

Quality Score

Status

Chromosome

Chromosomal Location

171416172-171434917 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 171429447 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Aspartic acid at position 103 (V103D)

Ref Sequence

ENSEMBL: ENSMUSP00000004827 (fasta)

Gene Model

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

AlphaFold

Q01965

Predicted Effect

possibly damaging
Transcript: ENSMUST00000004827
AA Change: V103D

PolyPhen 2 Score 0.650 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000004827
Gene: ENSMUSG00000004707
AA Change: V103D

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: V213D

PolyPhen 2 Score 0.081 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000069319
Gene: ENSMUSG00000004707
AA Change: V213D

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 benign
Transcript: ENSMUST00000111277
AA Change: V213D

PolyPhen 2 Score 0.066 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000106908
Gene: ENSMUSG00000004707
AA Change: V213D

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

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: 11 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5031410I06Rik	T	C	5: 26,309,153 (GRCm39)	R50G	probably damaging	Het
Atr	T	C	9: 95,747,105 (GRCm39)	V129A	probably damaging	Het
Bltp1	C	A	3: 36,962,367 (GRCm39)	H489Q	probably damaging	Het
Chd9	A	G	8: 91,712,760 (GRCm39)	E388G	probably damaging	Het
Crygd	C	T	1: 65,101,250 (GRCm39)	R115Q	probably benign	Het
Gabrg2	T	G	11: 41,862,599 (GRCm39)	I162L	possibly damaging	Het
Map3k9	G	A	12: 81,776,472 (GRCm39)	T603I	probably benign	Het
Mmrn1	T	C	6: 60,954,497 (GRCm39)	L926P	probably benign	Het
Scfd1	T	A	12: 51,436,098 (GRCm39)	D82E	probably benign	Het
Vangl1	T	A	3: 102,065,545 (GRCm39)		probably benign	Het
Vps13b	A	T	15: 35,417,723 (GRCm39)	I120L	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
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
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

Posted On

2012-12-06