Mutagenetix > Incidental Mutation

Incidental Mutation 'R1296:Nlgn3'

158167

Institutional Source

Beutler Lab

Gene Symbol

Nlgn3

Ensembl Gene

ENSMUSG00000031302

Gene Name

neuroligin 3

Synonyms

A230085M13Rik, NL3, NLG3, HNL3

MMRRC Submission

039362-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1296 (G1)

Quality Score

222

Status

Validated

Chromosome

Chromosomal Location

100342785-100364956 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

T to C at 100352522 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000123283 (fasta)

Gene Model

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

AlphaFold

Q8BYM5

Predicted Effect

probably benign
Transcript: ENSMUST00000065858

SMART Domains

Protein: ENSMUSP00000066304
Gene: ENSMUSG00000031302

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

noncoding transcript
Transcript: ENSMUST00000113671

Predicted Effect

probably benign
Transcript: ENSMUST00000118111

SMART Domains

Protein: ENSMUSP00000113863
Gene: ENSMUSG00000031302

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 benign
Transcript: ENSMUST00000130555

SMART Domains

Protein: ENSMUSP00000122213
Gene: ENSMUSG00000031302

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 benign
Transcript: ENSMUST00000151528

SMART Domains

Protein: ENSMUSP00000123283
Gene: ENSMUSG00000031302

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

0.0898

Coding Region Coverage

1x: 98.8%
3x: 97.7%
10x: 94.5%
20x: 87.1%

Validation Efficiency

100% (72/72)

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
Adam29	G	A	8: 56,324,754 (GRCm39)	Q567*	probably null	Het
Apol11a	T	C	15: 77,395,219 (GRCm39)		probably benign	Het
Arhgap29	A	G	3: 121,786,044 (GRCm39)	H275R	probably benign	Het
Arhgef17	C	A	7: 100,530,476 (GRCm39)	E428*	probably null	Het
Atm	A	T	9: 53,367,830 (GRCm39)	V2431E	probably damaging	Het
Atn1	G	T	6: 124,724,750 (GRCm39)	P161Q	unknown	Het
Atp13a2	T	C	4: 140,721,113 (GRCm39)	S99P	probably damaging	Het
Atp8a1	A	T	5: 67,780,049 (GRCm39)		probably benign	Het
Cdk18	T	C	1: 132,047,698 (GRCm39)		probably benign	Het
Cep85	A	G	4: 133,894,711 (GRCm39)	W32R	probably damaging	Het
Cntn4	G	T	6: 106,486,363 (GRCm39)	G264C	probably damaging	Het
Col6a4	A	G	9: 105,940,052 (GRCm39)	S1293P	possibly damaging	Het
Col6a6	T	C	9: 105,658,290 (GRCm39)	K641E	probably damaging	Het
Dmd	A	T	X: 82,922,126 (GRCm39)	K1465N	probably damaging	Het
Dus2	T	C	8: 106,779,675 (GRCm39)	V403A	possibly damaging	Het
Frs2	C	T	10: 116,916,979 (GRCm39)	C5Y	probably benign	Het
Gm5174	A	G	10: 86,492,866 (GRCm39)		noncoding transcript	Het
Gpr61	A	G	3: 108,057,797 (GRCm39)	V288A	possibly damaging	Het
Grik3	G	A	4: 125,598,357 (GRCm39)		probably benign	Het
Haao	T	A	17: 84,146,267 (GRCm39)	Q69L	probably benign	Het
Ints6	T	C	14: 62,942,352 (GRCm39)		probably benign	Het
Ints8	T	C	4: 11,221,204 (GRCm39)	I724V	possibly damaging	Het
Lrrk2	G	A	15: 91,613,123 (GRCm39)	C749Y	probably damaging	Het
Map4k1	A	G	7: 28,697,877 (GRCm39)	D471G	possibly damaging	Het
Mbtd1	A	G	11: 93,801,185 (GRCm39)	Y122C	probably damaging	Het
Mif-ps9	T	A	19: 56,743,766 (GRCm39)		noncoding transcript	Het
Mrfap1	A	G	5: 36,953,817 (GRCm39)	S41P	possibly damaging	Het
Mrm2	T	C	5: 140,314,308 (GRCm39)	T176A	probably benign	Het
Mslnl	T	C	17: 25,962,214 (GRCm39)	L204P	probably damaging	Het
Muc6	T	C	7: 141,238,144 (GRCm39)	E112G	probably benign	Het
Nfyb	A	G	10: 82,586,665 (GRCm39)		probably benign	Het
Nr3c1	G	A	18: 39,620,051 (GRCm39)	Q79*	probably null	Het
Nxpe4	C	G	9: 48,307,793 (GRCm39)	T299R	probably benign	Het
Otud4	C	A	8: 80,400,603 (GRCm39)	H1105N	unknown	Het
Pcnx2	A	G	8: 126,500,572 (GRCm39)	L1506P	probably damaging	Het
Prl2c5	T	A	13: 13,364,009 (GRCm39)	H88Q	probably damaging	Het
Psmb2	A	G	4: 126,580,825 (GRCm39)	Y73C	probably damaging	Het
Rbl1	A	T	2: 157,011,891 (GRCm39)	V688D	probably benign	Het
Rhox2g	C	A	X: 36,824,865 (GRCm39)		probably benign	Het
Rmnd5a	G	A	6: 71,375,439 (GRCm39)	L80F	probably benign	Het
Ryr2	T	C	13: 11,702,765 (GRCm39)		probably benign	Het
Sele	T	A	1: 163,878,379 (GRCm39)	S239R	probably damaging	Het
Siglecf	A	T	7: 43,005,344 (GRCm39)	R435*	probably null	Het
Slc23a1	C	T	18: 35,755,676 (GRCm39)	V407M	possibly damaging	Het
Slc6a14	G	A	X: 21,587,807 (GRCm39)	V122I	probably benign	Het
Spdl1	T	A	11: 34,704,434 (GRCm39)	E466D	unknown	Het
Stau2	A	G	1: 16,510,596 (GRCm39)	F121L	probably benign	Het
Stxbp1	A	T	2: 32,684,648 (GRCm39)	S594T	probably benign	Het
Sufu	G	A	19: 46,443,159 (GRCm39)		probably benign	Het
Tap2	G	T	17: 34,430,889 (GRCm39)	V330L	probably benign	Het
Tbc1d1	T	C	5: 64,421,775 (GRCm39)	L389P	probably damaging	Het
Tbx2	A	G	11: 85,725,592 (GRCm39)	E181G	probably damaging	Het
Tlcd4	A	G	3: 121,000,940 (GRCm39)	V231A	probably benign	Het
Tmprss9	G	T	10: 80,726,279 (GRCm39)	A510S	probably benign	Het
Tnxb	G	A	17: 34,890,551 (GRCm39)	C298Y	probably damaging	Het
Tril	G	T	6: 53,795,012 (GRCm39)	R737S	probably damaging	Het
Ugt2a3	A	T	5: 87,475,005 (GRCm39)	L413Q	probably damaging	Het
Vcan	A	G	13: 89,805,675 (GRCm39)	I2335T	probably damaging	Het
Vmn2r28	T	C	7: 5,484,544 (GRCm39)	N552S	possibly damaging	Het
Zc3h7a	C	T	16: 10,978,890 (GRCm39)	R95H	probably damaging	Het
Zfp598	A	G	17: 24,898,623 (GRCm39)	N474S	probably benign	Het
Zng1	A	T	19: 24,920,039 (GRCm39)		probably benign	Het
Zpld1	T	C	16: 55,068,697 (GRCm39)	D138G	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
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
R9231: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'- GACATCCGAGACAGTGGTGCTAAAC -3'
(R):5'- AAATCTGCTAACAGAAGTCTGGCTGAG -3'

Sequencing Primer
(F):5'- ACAGTGGTGCTAAACCTGTC -3'
(R):5'- tcagggaggtagaagtaggaag -3'

Posted On

2014-02-18