Mutagenetix > Incidental Mutation

Incidental Mutation 'R9231:Nlgn3'

700272

Institutional Source

Beutler Lab

Gene Symbol

Nlgn3

Ensembl Gene

ENSMUSG00000031302

Gene Name

neuroligin 3

Synonyms

A230085M13Rik, NL3, NLG3, HNL3

MMRRC Submission

068985-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9231 (G1)

Quality Score

221.999

Status

Validated

Chromosome

Chromosomal Location

100342785-100364956 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 100352390 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 179 (V179A)

Ref Sequence

ENSEMBL: ENSMUSP00000066304 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000065858] [ENSMUST00000118111] [ENSMUST00000130555] [ENSMUST00000151528]

AlphaFold

Q8BYM5

Predicted Effect

probably damaging
Transcript: ENSMUST00000065858
AA Change: V179A

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

SMART Domains

Protein: ENSMUSP00000066304
Gene: ENSMUSG00000031302
AA Change: V179A

Domain	Start	End	E-Value	Type
Pfam:COesterase	16	601	2.3e-194	PFAM
Pfam:Abhydrolase_3	180	342	1.7e-7	PFAM
transmembrane domain	685	707	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000118111
AA Change: V65A

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

SMART Domains

Protein: ENSMUSP00000113863
Gene: ENSMUSG00000031302
AA Change: V65A

Domain	Start	End	E-Value	Type
Pfam:COesterase	3	487	3.6e-161	PFAM
Pfam:Abhydrolase_3	66	232	2.4e-7	PFAM
transmembrane domain	571	593	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000130555
AA Change: V159A

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

SMART Domains

Protein: ENSMUSP00000122213
Gene: ENSMUSG00000031302
AA Change: V159A

Domain	Start	End	E-Value	Type
Pfam:COesterase	16	510	4.6e-179	PFAM
Pfam:Abhydrolase_3	160	323	1.5e-7	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000151528
AA Change: V199A

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

SMART Domains

Protein: ENSMUSP00000123283
Gene: ENSMUSG00000031302
AA Change: V199A

Domain	Start	End	E-Value	Type
Pfam:COesterase	16	621	3.4e-207	PFAM
Pfam:Abhydrolase_3	200	363	1.2e-6	PFAM
transmembrane domain	705	727	N/A	INTRINSIC

Meta Mutation Damage Score

0.9671

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.9%
20x: 99.7%

Validation Efficiency

98% (60/61)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of a family of neuronal cell surface proteins. Members of this family may act as splice site-specific ligands for beta-neurexins and may be involved in the formation and remodeling of central nervous system synapses. Mutations in this gene may be associated with autism and Asperger syndrome. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Oct 2009]
PHENOTYPE: Homozygous null mice show impaired context and cued conditioning, hyperactivity, altered social behavior, less vocalization, smaller brains, and impaired olfaction. Males carrying a knock-in allele show impaired social interaction, and enhanced spatial learning and inhibitory synaptic transmission. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acacb	A	G	5: 114,349,153 (GRCm39)	Q1073R	probably benign	Het
Akirin2	A	G	4: 34,551,072 (GRCm39)	T10A	possibly damaging	Het
Ankrd13a	T	A	5: 114,942,295 (GRCm39)	I526N	probably damaging	Het
Ankrd28	A	G	14: 31,429,234 (GRCm39)	V876A	possibly damaging	Het
Aqp8	T	A	7: 123,061,813 (GRCm39)	M11K	probably benign	Het
Catsper3	T	C	13: 55,946,705 (GRCm39)	I134T	possibly damaging	Het
Cdk9	G	T	2: 32,598,006 (GRCm39)	T350N	probably benign	Het
Ckmt2	G	T	13: 92,011,311 (GRCm39)	H100N	probably damaging	Het
Cnnm4	A	T	1: 36,511,258 (GRCm39)	D162V	probably benign	Het
Cnppd1	T	C	1: 75,116,261 (GRCm39)	H108R	possibly damaging	Het
Col17a1	G	A	19: 47,667,861 (GRCm39)	R139*	probably null	Het
Cyp2c65	C	T	19: 39,060,661 (GRCm39)	P174S	possibly damaging	Het
Dync2li1	A	G	17: 84,935,819 (GRCm39)	S39G	probably null	Het
Ecpas	A	G	4: 58,875,533 (GRCm39)	Y144H	probably damaging	Het
Eif2ak4	A	G	2: 118,271,662 (GRCm39)	D882G	probably benign	Het
Emp1	C	T	6: 135,354,276 (GRCm39)	T23I	probably damaging	Het
Epha8	T	A	4: 136,673,226 (GRCm39)	D186V	probably damaging	Het
Fam169a	T	G	13: 97,254,967 (GRCm39)	D394E	probably benign	Het
Fam20b	T	C	1: 156,509,084 (GRCm39)	D376G	probably benign	Het
Fgfbp3	C	T	19: 36,896,193 (GRCm39)	A142T	possibly damaging	Het
Flg2	C	T	3: 93,109,508 (GRCm39)	S512L	unknown	Het
Fras1	T	A	5: 96,692,904 (GRCm39)	C188S	probably damaging	Het
Galr2	T	C	11: 116,174,335 (GRCm39)	C322R	probably benign	Het
Gbe1	T	A	16: 70,284,989 (GRCm39)	M437K	possibly damaging	Het
Glt1d1	T	A	5: 127,754,341 (GRCm39)	L181Q	probably damaging	Het
Gpr180	G	A	14: 118,395,455 (GRCm39)	V296I	probably damaging	Het
Gucy1a1	C	T	3: 82,013,308 (GRCm39)	E445K	probably damaging	Het
H2-T24	T	C	17: 36,331,363 (GRCm39)	D14G	possibly damaging	Het
Igsf10	G	A	3: 59,243,843 (GRCm39)	R164W	probably damaging	Het
Ing5	T	G	1: 93,739,505 (GRCm39)	D37E	probably benign	Het
Kcnt1	A	G	2: 25,801,074 (GRCm39)	T1051A	probably benign	Het
Kif1b	A	T	4: 149,275,652 (GRCm39)	S1420T	possibly damaging	Het
Klk15	C	T	7: 43,587,790 (GRCm39)	H73Y	possibly damaging	Het
Kmt2a	A	G	9: 44,759,912 (GRCm39)	F646L	probably damaging	Het
Lrp1	T	C	10: 127,382,268 (GRCm39)	D3731G	probably benign	Het
Mif	T	A	10: 75,695,370 (GRCm39)	I97F	probably damaging	Het
Mpp4	A	T	1: 59,163,833 (GRCm39)	V507D	probably damaging	Het
Mrpl1	C	A	5: 96,361,719 (GRCm39)	N35K	probably benign	Het
Naf1	CGCCAGCCCCGAGCTCGGATCCCGGCGGAAGACCACCGCCGCTGCCAGCCCCGAGCTCGGATCCCGGCGGAAGACCACCGCCGCTGCCAGCCCCGAACTCGGATCCCGGCGGAAGACCACCGCCGCTGCCAGCCCCGAGCTCGGATCCCGGCGGAAGACCACCGCCGCTGCCAGCCCCGAACTCGGATCCCGGCGGAAGACCACCGCCGCTGCCAGCCCCGAGCTCGGATCCCGGCGGAAGACCACCGCCGCTGCCAGCCCCGAACTCGGATCCCGGCGGAAGACCACCGCCGCCGCCAGCCCCGAGCTCGGATCCCGGCGGAAGACCACCGCCGCCGCCAGCCCCGA	CGCCAGCCCCGAGCTCGGATCCCGGCGGAAGACCACCGCCGCTGCCAGCCCCGAACTCGGATCCCGGCGGAAGACCACCGCCGCTGCCAGCCCCGAGCTCGGATCCCGGCGGAAGACCACCGCCGCTGCCAGCCCCGAACTCGGATCCCGGCGGAAGACCACCGCCGCTGCCAGCCCCGAGCTCGGATCCCGGCGGAAGACCACCGCCGCTGCCAGCCCCGAACTCGGATCCCGGCGGAAGACCACCGCCGCCGCCAGCCCCGAGCTCGGATCCCGGCGGAAGACCACCGCCGCCGCCAGCCCCGA	8: 67,313,146 (GRCm39)		probably benign	Het
Nat8f6	A	G	6: 85,785,630 (GRCm39)	V173A	probably damaging	Het
Ninl	C	T	2: 150,792,129 (GRCm39)	R798Q	probably benign	Het
Or10a49	T	C	7: 108,467,840 (GRCm39)	I174V	possibly damaging	Het
Or1af1	A	T	2: 37,109,989 (GRCm39)	M163L	possibly damaging	Het
Paqr8	A	G	1: 21,005,875 (GRCm39)	H343R	probably benign	Het
Parp14	A	G	16: 35,661,583 (GRCm39)	V1455A	probably damaging	Het
Parp3	A	T	9: 106,350,891 (GRCm39)	S334T	probably benign	Het
Pcbp2	T	G	15: 102,394,477 (GRCm39)		probably null	Het
Perm1	A	T	4: 156,302,234 (GRCm39)	E259D	probably damaging	Het
Plce1	A	T	19: 38,705,040 (GRCm39)	N815I	probably benign	Het
Plxnb1	A	T	9: 108,934,286 (GRCm39)	D838V	possibly damaging	Het
Prdm12	A	G	2: 31,530,265 (GRCm39)	D52G	probably benign	Het
Rac2	T	C	15: 78,450,223 (GRCm39)	N39S	probably damaging	Het
Smchd1	A	T	17: 71,672,084 (GRCm39)	C1657S	probably benign	Het
Sugct	T	A	13: 17,627,071 (GRCm39)	T261S	probably damaging	Het
Tbc1d10a	T	C	11: 4,164,885 (GRCm39)	L446P	probably damaging	Het
Tcp1	T	A	17: 13,136,761 (GRCm39)	D47E	probably damaging	Het
Tenm3	T	A	8: 48,689,231 (GRCm39)	T2119S	probably damaging	Het
Tent5a	T	G	9: 85,208,388 (GRCm39)	D145A	possibly damaging	Het
Tmem132b	T	C	5: 125,860,531 (GRCm39)	M592T	probably damaging	Het
Trim28	G	A	7: 12,763,490 (GRCm39)	A544T	probably benign	Het
Vinac1	A	T	2: 128,879,340 (GRCm39)	I862N	unknown	Het
Washc2	C	A	6: 116,235,899 (GRCm39)	D1123E	probably benign	Het
Wee2	A	G	6: 40,440,089 (GRCm39)	I412M	probably damaging	Het

Other mutations in Nlgn3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01128:Nlgn3	APN	X	100,363,698 (GRCm39)	missense	probably benign	0.28
IGL01327:Nlgn3	APN	X	100,362,228 (GRCm39)	missense	probably benign	0.08
IGL01414:Nlgn3	APN	X	100,345,866 (GRCm39)	missense	probably benign	0.00
R1296:Nlgn3	UTSW	X	100,352,522 (GRCm39)	splice site	probably benign
R1794:Nlgn3	UTSW	X	100,363,639 (GRCm39)	missense	probably benign	0.30
R5144:Nlgn3	UTSW	X	100,361,891 (GRCm39)	missense	probably benign	0.21
R5145:Nlgn3	UTSW	X	100,361,891 (GRCm39)	missense	probably benign	0.21
R5146:Nlgn3	UTSW	X	100,361,891 (GRCm39)	missense	probably benign	0.21
R8677:Nlgn3	UTSW	X	100,352,390 (GRCm39)	missense	probably damaging	1.00
R8678:Nlgn3	UTSW	X	100,352,390 (GRCm39)	missense	probably damaging	1.00
R8684:Nlgn3	UTSW	X	100,363,425 (GRCm39)	nonsense	probably null
R8696:Nlgn3	UTSW	X	100,352,390 (GRCm39)	missense	probably damaging	1.00
R8905:Nlgn3	UTSW	X	100,352,390 (GRCm39)	missense	probably damaging	1.00
R8906:Nlgn3	UTSW	X	100,352,390 (GRCm39)	missense	probably damaging	1.00
R9232:Nlgn3	UTSW	X	100,352,390 (GRCm39)	missense	probably damaging	1.00
R9234:Nlgn3	UTSW	X	100,352,390 (GRCm39)	missense	probably damaging	1.00
R9235:Nlgn3	UTSW	X	100,352,390 (GRCm39)	missense	probably damaging	1.00
R9236:Nlgn3	UTSW	X	100,352,390 (GRCm39)	missense	probably damaging	1.00
R9253:Nlgn3	UTSW	X	100,352,390 (GRCm39)	missense	probably damaging	1.00
Z1176:Nlgn3	UTSW	X	100,363,483 (GRCm39)	missense	probably damaging	1.00
Z1176:Nlgn3	UTSW	X	100,361,588 (GRCm39)	missense	probably benign	0.30

Predicted Primers

PCR Primer
(F):5'- TGGCCAGTACTTCAACTCCG -3'
(R):5'- TTAACACCAGCGAGAGATCTAGGAC -3'

Sequencing Primer
(F):5'- AGTACTTCAACTCCGGGCCTAG -3'
(R):5'- AGGACTACCTAAATTGACTTCCCTGG -3'

Posted On

2022-02-07