Mutagenetix > Incidental Mutation

Incidental Mutation 'R8905:Nlgn3'

680069

Institutional Source

Beutler Lab

Gene Symbol

Nlgn3

Ensembl Gene

ENSMUSG00000031302

Gene Name

neuroligin 3

Synonyms

A230085M13Rik, NL3, NLG3, HNL3

MMRRC Submission

068762-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8905 (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: 99.9%
10x: 99.5%
20x: 98.3%

Validation Efficiency

100% (77/77)

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700013G24Rik	T	C	4: 137,182,553 (GRCm39)	V236A	probably benign	Het
Abca15	A	T	7: 119,960,771 (GRCm39)	R744S	probably benign	Het
Adgra1	T	C	7: 139,455,763 (GRCm39)	S464P	probably damaging	Het
Arhgap45	T	C	10: 79,855,570 (GRCm39)	V3A	probably benign	Het
AW554918	T	A	18: 25,473,206 (GRCm39)	S134T	probably damaging	Het
Bmper	A	G	9: 23,318,082 (GRCm39)	E567G	probably benign	Het
C2cd3	T	C	7: 100,074,132 (GRCm39)		probably null	Het
Cars1	A	G	7: 143,140,196 (GRCm39)	Y170H	probably damaging	Het
Celsr1	A	T	15: 85,788,269 (GRCm39)		probably benign	Het
Celsr3	C	T	9: 108,718,501 (GRCm39)	H2351Y	probably damaging	Het
Cfap210	A	G	2: 69,612,104 (GRCm39)	S175P	probably benign	Het
Clxn	A	G	16: 14,738,275 (GRCm39)	I147V	possibly damaging	Het
Cyp2d11	T	C	15: 82,275,102 (GRCm39)	I282V	probably benign	Het
Dhfr	A	G	13: 92,494,467 (GRCm39)	T57A	probably damaging	Het
Dhrs7l	T	A	12: 72,666,431 (GRCm39)	D80V	probably damaging	Het
Dnah7b	A	C	1: 46,292,534 (GRCm39)	Q2973P	probably damaging	Het
Dnajc5b	T	C	3: 19,633,184 (GRCm39)	C136R	probably benign	Het
Ercc3	T	G	18: 32,398,771 (GRCm39)	D683E	possibly damaging	Het
Faxc	A	G	4: 21,982,398 (GRCm39)	Y279C	probably damaging	Het
Fbxw7	T	C	3: 84,872,634 (GRCm39)	M191T	possibly damaging	Het
Fcgbp	T	A	7: 27,785,934 (GRCm39)	V457E	probably damaging	Het
Fip1l1	A	T	5: 74,756,624 (GRCm39)	T539S	probably damaging	Het
Gabra1	T	C	11: 42,038,052 (GRCm39)	T189A	possibly damaging	Het
Glg1	T	C	8: 111,884,668 (GRCm39)	D1118G	probably damaging	Het
Gli3	A	G	13: 15,901,116 (GRCm39)	D1501G	probably benign	Het
Hacd1	A	G	2: 14,049,761 (GRCm39)	I91T	possibly damaging	Het
Ift22	T	C	5: 136,941,745 (GRCm39)	V159A	probably benign	Het
Igkv1-110	T	A	6: 68,248,070 (GRCm39)	Y60N	probably damaging	Het
Inpp5d	A	G	1: 87,637,348 (GRCm39)	K502E	probably damaging	Het
Kcnt2	A	T	1: 140,435,467 (GRCm39)	Q478L	possibly damaging	Het
Mettl13	A	G	1: 162,364,847 (GRCm39)	F511L	probably damaging	Het
Mis18bp1	T	C	12: 65,180,401 (GRCm39)		probably null	Het
Mrps30	A	T	13: 118,523,479 (GRCm39)	S98T	probably benign	Het
Muc2	C	T	7: 141,279,643 (GRCm39)	A209V	probably benign	Het
Nfs1	A	T	2: 155,970,503 (GRCm39)	I270N	probably damaging	Het
Nsmaf	A	G	4: 6,424,951 (GRCm39)	S266P	probably benign	Het
Obscn	A	G	11: 58,960,784 (GRCm39)	S3176P	probably damaging	Het
Or4c123	A	T	2: 89,126,801 (GRCm39)	L271Q	possibly damaging	Het
Or7g12	A	G	9: 18,899,494 (GRCm39)	D70G	possibly damaging	Het
P2ry12	T	A	3: 59,124,997 (GRCm39)	Y226F	probably damaging	Het
Pabpc2	C	A	18: 39,907,704 (GRCm39)	T323K	probably benign	Het
Pank2	A	G	2: 131,124,646 (GRCm39)	D71G	possibly damaging	Het
Patj	A	T	4: 98,385,412 (GRCm39)	H393L	probably damaging	Het
Pde8b	A	G	13: 95,182,993 (GRCm39)	V255A	probably damaging	Het
Plekhs1	T	C	19: 56,471,028 (GRCm39)	W374R	probably damaging	Het
Ppm1g	T	C	5: 31,361,437 (GRCm39)	D313G	probably damaging	Het
Rnf114	A	G	2: 167,353,134 (GRCm39)	N135S	probably benign	Het
Rnf43	T	G	11: 87,621,951 (GRCm39)	Y351D	probably damaging	Het
Robo1	A	T	16: 72,539,173 (GRCm39)	D90V	probably damaging	Het
Sbds	A	G	5: 130,277,125 (GRCm39)	V172A	possibly damaging	Het
Scamp5	T	A	9: 57,352,669 (GRCm39)	I167F	probably benign	Het
Sec14l5	A	G	16: 4,994,364 (GRCm39)	E386G	probably damaging	Het
Sfxn1	T	A	13: 54,246,433 (GRCm39)	V159E	probably damaging	Het
Sgsm1	C	T	5: 113,421,495 (GRCm39)	G531R	probably benign	Het
Slc22a26	T	A	19: 7,760,331 (GRCm39)	I471F	probably damaging	Het
Slc41a3	T	A	6: 90,589,123 (GRCm39)	M78K	probably benign	Het
Slc8a1	A	T	17: 81,749,084 (GRCm39)	Y653N	probably benign	Het
Slco6c1	A	T	1: 97,053,391 (GRCm39)	M170K	possibly damaging	Het
Smarca5	A	T	8: 81,440,577 (GRCm39)	I629K	probably benign	Het
Smg7	T	A	1: 152,715,817 (GRCm39)	D1099V	probably damaging	Het
Spata31e2	A	G	1: 26,721,895 (GRCm39)	V1095A	probably damaging	Het
Srbd1	T	C	17: 86,308,890 (GRCm39)	I763V	probably benign	Het
Stk25	A	G	1: 93,556,929 (GRCm39)	S30P	probably damaging	Het
Sv2b	C	T	7: 74,767,459 (GRCm39)	A646T	probably benign	Het
Tardbp	T	C	4: 148,705,093 (GRCm39)	M167V	probably benign	Het
Tmem132a	T	C	19: 10,842,647 (GRCm39)	N276S	probably damaging	Het
Ttpa	T	A	4: 20,028,435 (GRCm39)	S162T	probably benign	Het
Usp13	T	C	3: 32,935,572 (GRCm39)	Y333H	probably damaging	Het
Vmn2r3	T	A	3: 64,166,695 (GRCm39)	Y812F	probably damaging	Het
Yeats2	A	G	16: 20,009,144 (GRCm39)	T463A	probably benign	Het
Zbtb26	T	A	2: 37,326,927 (GRCm39)	K36N	probably benign	Het
Zfc3h1	A	T	10: 115,259,383 (GRCm39)	T1652S	probably benign	Het
Zfp472	G	A	17: 33,197,455 (GRCm39)	C510Y	possibly damaging	Het
Zfp518a	C	A	19: 40,902,780 (GRCm39)	T903K	probably damaging	Het
Zfp668	T	C	7: 127,465,598 (GRCm39)	T529A	probably benign	Het
Zfp930	A	G	8: 69,681,351 (GRCm39)	T349A	possibly damaging	Het
Zmiz2	T	G	11: 6,346,840 (GRCm39)	Y182D	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
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'- TGGCCAGTACTTCAACTCCG -3'
(R):5'- TTAACACCAGCGAGAGATCTAG -3'

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

Posted On

2021-08-31