Mutagenetix > Incidental Mutation

Incidental Mutation 'R9253:Nlgn3'

701695

Institutional Source

Beutler Lab

Gene Symbol

Nlgn3

Ensembl Gene

ENSMUSG00000031302

Gene Name

neuroligin 3

Synonyms

A230085M13Rik, NL3, NLG3, HNL3

MMRRC Submission

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9253 (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: 99.8%
20x: 99.2%

Validation Efficiency

100% (63/63)

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: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts19	A	G	18: 59,103,013 (GRCm39)	N685D	probably damaging	Het
Adh4	A	T	3: 138,129,860 (GRCm39)	I229F	probably damaging	Het
Ajm1	T	C	2: 25,467,172 (GRCm39)	H913R	possibly damaging	Het
Aldh3b1	T	A	19: 3,965,315 (GRCm39)	S399C	probably damaging	Het
Arhgef28	C	T	13: 98,124,779 (GRCm39)	G501D	probably benign	Het
Asb1	C	A	1: 91,468,551 (GRCm39)	T6N	unknown	Het
Asb18	C	T	1: 89,882,185 (GRCm39)	V382I	probably benign	Het
AU041133	T	C	10: 81,987,220 (GRCm39)	I291T	probably benign	Het
B4galnt2	C	T	11: 95,759,176 (GRCm39)		silent	Het
Bcl7c	T	C	7: 127,306,403 (GRCm39)		probably benign	Het
Brinp1	T	C	4: 68,711,083 (GRCm39)	N375S	possibly damaging	Het
C6	A	G	15: 4,764,679 (GRCm39)	Q125R	probably benign	Het
Card14	T	C	11: 119,212,759 (GRCm39)	S108P	probably benign	Het
Clec4a2	C	A	6: 123,100,608 (GRCm39)	T21N	probably damaging	Het
Cntnap2	C	T	6: 45,978,112 (GRCm39)	L256F	probably benign	Het
Cobll1	G	A	2: 64,981,503 (GRCm39)	T29I	probably benign	Het
Coq4	A	T	2: 29,685,433 (GRCm39)	D149V	probably damaging	Het
Dync1i1	T	C	6: 5,769,698 (GRCm39)	L91S	probably benign	Het
Fat2	T	A	11: 55,201,397 (GRCm39)	D559V	probably damaging	Het
Gm4779	TGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAG	TGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAGAGGCAG	X: 100,836,917 (GRCm39)		probably benign	Het
Gsdmc	A	T	15: 63,676,407 (GRCm39)	V12E	probably damaging	Het
H2-Ab1	T	C	17: 34,486,378 (GRCm39)	S146P	probably damaging	Het
Heatr5b	A	G	17: 79,135,423 (GRCm39)	V236A	probably benign	Het
Hjv	T	C	3: 96,435,710 (GRCm39)	S323P	probably benign	Het
Hmgcr	C	T	13: 96,796,645 (GRCm39)	C215Y	probably damaging	Het
L3mbtl1	G	T	2: 162,789,632 (GRCm39)	A57S	probably benign	Het
Lilrb4b	G	A	10: 51,357,863 (GRCm39)	V186I	probably damaging	Het
Map1a	T	C	2: 121,132,823 (GRCm39)	V1213A	probably benign	Het
Marf1	T	C	16: 13,935,172 (GRCm39)	E1532G	probably damaging	Het
Mcm6	T	C	1: 128,279,264 (GRCm39)	Y174C	probably damaging	Het
Miga2	T	A	2: 30,261,239 (GRCm39)	V178E	probably benign	Het
Myh11	T	A	16: 14,074,359 (GRCm39)	I174F		Het
Ndufv1	G	T	19: 4,059,412 (GRCm39)	A211E	probably damaging	Het
Nicn1	C	T	9: 108,171,708 (GRCm39)	R163C	possibly damaging	Het
Nrp1	T	C	8: 129,229,144 (GRCm39)	V874A	possibly damaging	Het
Nsf	C	T	11: 103,804,142 (GRCm39)	G197S	probably null	Het
Or10al2	A	T	17: 37,983,637 (GRCm39)	H241L	probably benign	Het
Or2t26	T	C	11: 49,039,822 (GRCm39)	M246T	probably damaging	Het
Pacs2	A	G	12: 113,014,137 (GRCm39)	D196G	probably benign	Het
Pbxip1	A	G	3: 89,351,012 (GRCm39)	D118G	probably benign	Het
Pcdhb11	A	T	18: 37,554,529 (GRCm39)		probably benign	Het
Pgk2	C	T	17: 40,519,233 (GRCm39)	G65D	probably damaging	Het
Plcd3	T	C	11: 102,970,460 (GRCm39)	D193G	probably benign	Het
Plcl2	T	G	17: 50,915,127 (GRCm39)	M712R	probably damaging	Het
Plxna1	G	A	6: 89,334,522 (GRCm39)	Q36*	probably null	Het
Plxnb2	A	G	15: 89,052,015 (GRCm39)	V68A	probably benign	Het
Polr2b	A	G	5: 77,493,224 (GRCm39)	I1069V	probably benign	Het
Rbfox1	A	G	16: 7,111,973 (GRCm39)	T200A	probably benign	Het
Rspry1	T	A	8: 95,349,621 (GRCm39)	V3D	probably damaging	Het
Serpinb6d	T	C	13: 33,855,205 (GRCm39)	M293T	probably damaging	Het
Slc4a8	A	G	15: 100,680,913 (GRCm39)	R72G	probably benign	Het
Smarca5	A	C	8: 81,446,344 (GRCm39)	L452W	probably damaging	Het
Srcin1	T	C	11: 97,416,377 (GRCm39)	K952E	probably damaging	Het
Synpo2l	G	T	14: 20,716,738 (GRCm39)	Q79K	possibly damaging	Het
Tmem174	T	C	13: 98,773,803 (GRCm39)	E9G	possibly damaging	Het
Tmem270	T	C	5: 134,930,644 (GRCm39)	T206A	probably damaging	Het
Ttn	T	A	2: 76,562,951 (GRCm39)	T28668S	possibly damaging	Het
Vmn1r118	A	T	7: 20,645,817 (GRCm39)	S152R	possibly damaging	Het
Vmn2r25	T	A	6: 123,816,960 (GRCm39)	Q207L	probably damaging	Het
Vmn2r81	T	A	10: 79,129,582 (GRCm39)	S824R	probably damaging	Het
Vps54	G	A	11: 21,258,771 (GRCm39)	V733I	probably benign	Het
Zfp518b	G	T	5: 38,829,601 (GRCm39)	D801E	probably benign	Het
Zgrf1	C	A	3: 127,392,428 (GRCm39)	P1316Q	probably damaging	Het
Zzef1	C	A	11: 72,739,463 (GRCm39)		probably benign	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
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
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'- TCTGGCCAGTACTTCAACTCCG -3'
(R):5'- TAACACCAGCGAGAGATCTAGG -3'

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

Posted On

2022-03-25