Mutagenetix > Incidental Mutation

Incidental Mutation 'R3056:Nlgn1'

265167

Institutional Source

Beutler Lab

Gene Symbol

Nlgn1

Ensembl Gene

ENSMUSG00000063887

Gene Name

neuroligin 1

Synonyms

NL1, Nlg1, 6330415N05Rik

MMRRC Submission

040565-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R3056 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

25480379-26386609 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 25487860 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 825 (N825S)

Ref Sequence

ENSEMBL: ENSMUSP00000142200 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000075054] [ENSMUST00000108308] [ENSMUST00000191835] [ENSMUST00000193603]

AlphaFold

Q99K10

PDB Structure

Crystal structure of a synaptic adhesion complex [X-RAY DIFFRACTION]

Predicted Effect

possibly damaging
Transcript: ENSMUST00000075054
AA Change: N825S

PolyPhen 2 Score 0.528 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000074565
Gene: ENSMUSG00000063887
AA Change: N825S

Domain	Start	End	E-Value	Type
Pfam:COesterase	29	626	4.8e-199	PFAM
Pfam:Abhydrolase_3	196	302	2.2e-8	PFAM
transmembrane domain	697	719	N/A	INTRINSIC
low complexity region	720	731	N/A	INTRINSIC
low complexity region	796	809	N/A	INTRINSIC
low complexity region	816	827	N/A	INTRINSIC
low complexity region	829	839	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000108308
AA Change: N796S

SMART Domains

Protein: ENSMUSP00000103944
Gene: ENSMUSG00000063887
AA Change: N796S

Domain	Start	End	E-Value	Type
Pfam:COesterase	29	597	2.5e-190	PFAM
Pfam:Abhydrolase_3	176	306	4.3e-8	PFAM
transmembrane domain	668	690	N/A	INTRINSIC
low complexity region	691	702	N/A	INTRINSIC
low complexity region	767	780	N/A	INTRINSIC
low complexity region	787	798	N/A	INTRINSIC
low complexity region	800	810	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000191835
AA Change: N796S

SMART Domains

Protein: ENSMUSP00000142086
Gene: ENSMUSG00000063887
AA Change: N796S

Domain	Start	End	E-Value	Type
Pfam:COesterase	29	597	2.5e-190	PFAM
Pfam:Abhydrolase_3	176	306	4.3e-8	PFAM
transmembrane domain	668	690	N/A	INTRINSIC
low complexity region	691	702	N/A	INTRINSIC
low complexity region	767	780	N/A	INTRINSIC
low complexity region	787	798	N/A	INTRINSIC
low complexity region	800	810	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000193603
AA Change: N825S

PolyPhen 2 Score 0.528 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887
AA Change: N825S

Domain	Start	End	E-Value	Type
Pfam:COesterase	29	626	1.2e-186	PFAM
Pfam:Abhydrolase_3	196	309	3.7e-8	PFAM
transmembrane domain	697	719	N/A	INTRINSIC
low complexity region	720	731	N/A	INTRINSIC
low complexity region	796	809	N/A	INTRINSIC
low complexity region	816	827	N/A	INTRINSIC
low complexity region	829	839	N/A	INTRINSIC

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.8%

Validation Efficiency

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. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele are viable and fertile but display impaired NMDA receptor-mediated synaptic transmission onto CA1 pyramidal cells. [provided by MGI curators]

Allele List at MGI

All alleles(4) : Targeted(3) Gene trapped(1)

Other mutations in this stock

Total: 39 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadacl4fm4	A	G	4: 144,401,268 (GRCm39)	I72T	probably benign	Het
Abca1	A	T	4: 53,127,626 (GRCm39)	M131K	probably benign	Het
Agbl1	C	T	7: 76,416,232 (GRCm39)	T751M	possibly damaging	Het
Asb14	A	G	14: 26,636,146 (GRCm39)	I510V	possibly damaging	Het
Bard1	A	G	1: 71,127,390 (GRCm39)	V73A	possibly damaging	Het
C6	T	C	15: 4,769,355 (GRCm39)	I187T	probably damaging	Het
Catsper3	T	C	13: 55,956,709 (GRCm39)	S376P	unknown	Het
Ccdc150	A	G	1: 54,328,001 (GRCm39)	N361S	possibly damaging	Het
Cntn5	A	G	9: 10,419,076 (GRCm39)	L7P	probably benign	Het
Cplane1	T	C	15: 8,280,491 (GRCm39)	S2805P	unknown	Het
Cxcr6	A	T	9: 123,639,529 (GRCm39)	I177F	probably damaging	Het
Dnah7b	A	G	1: 46,307,869 (GRCm39)	D3061G	possibly damaging	Het
Epas1	T	C	17: 87,138,409 (GRCm39)	F835S	probably damaging	Het
Fat3	C	T	9: 15,871,792 (GRCm39)	R3533H	probably benign	Het
Fxr1	A	G	3: 34,103,333 (GRCm39)	E221G	probably damaging	Het
Gpatch11	A	G	17: 79,151,272 (GRCm39)	T228A	probably damaging	Het
Greb1	G	T	12: 16,738,592 (GRCm39)	T1457K	probably damaging	Het
Ighm	T	A	12: 113,382,596 (GRCm39)		probably benign	Het
Ints12	G	A	3: 132,815,126 (GRCm39)	M444I	possibly damaging	Het
Lmx1b	G	A	2: 33,457,297 (GRCm39)	Q168*	probably null	Het
Ltbp3	C	A	19: 5,801,434 (GRCm39)	N659K	probably benign	Het
Micos13	A	G	17: 56,915,889 (GRCm39)	F55S	probably damaging	Het
Mrpl20	G	T	4: 155,888,329 (GRCm39)	V43F	possibly damaging	Het
Or5d36	T	A	2: 87,901,583 (GRCm39)	T48S	probably benign	Het
Or5p67	A	T	7: 107,922,757 (GRCm39)	V42E	possibly damaging	Het
Or8k3b	C	A	2: 86,520,896 (GRCm39)	C141F	possibly damaging	Het
Pccb	C	T	9: 100,912,250 (GRCm39)	R79Q	probably damaging	Het
Peg10	G	A	6: 4,755,029 (GRCm39)	R270H	possibly damaging	Het
Pttg1ip2	A	T	5: 5,507,283 (GRCm39)		probably null	Het
Rufy4	T	C	1: 74,186,822 (GRCm39)	C537R	probably damaging	Het
Slc4a4	T	C	5: 89,373,807 (GRCm39)	V971A	probably damaging	Het
Timm29	T	C	9: 21,504,887 (GRCm39)	M185T	probably damaging	Het
Tmem92	C	T	11: 94,669,873 (GRCm39)	C86Y	probably benign	Het
Tnfrsf8	C	T	4: 145,011,895 (GRCm39)		probably null	Het
Tnks1bp1	T	A	2: 84,900,344 (GRCm39)	C1433*	probably null	Het
Utp14b	T	A	1: 78,642,442 (GRCm39)	D113E	possibly damaging	Het
Vmn2r110	T	A	17: 20,803,360 (GRCm39)	Y405F	probably damaging	Het
Wiz	A	G	17: 32,576,671 (GRCm39)	S628P	probably benign	Het
Xrcc4	T	C	13: 90,210,196 (GRCm39)	T83A	probably benign	Het

Other mutations in Nlgn1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00510:Nlgn1	APN	3	25,490,654 (GRCm39)	missense	probably benign	0.02
IGL00543:Nlgn1	APN	3	25,487,945 (GRCm39)	missense	probably damaging	1.00
IGL00960:Nlgn1	APN	3	25,966,861 (GRCm39)	missense	probably damaging	1.00
IGL01533:Nlgn1	APN	3	25,490,527 (GRCm39)	missense	possibly damaging	0.69
IGL02146:Nlgn1	APN	3	25,966,846 (GRCm39)	missense	probably damaging	0.96
IGL02616:Nlgn1	APN	3	25,488,409 (GRCm39)	missense	probably damaging	0.99
IGL03342:Nlgn1	APN	3	26,187,411 (GRCm39)	missense	probably damaging	1.00
ligation	UTSW	3	25,490,199 (GRCm39)	nonsense	probably null
G1citation:Nlgn1	UTSW	3	26,187,796 (GRCm39)	missense	probably benign	0.00
P0018:Nlgn1	UTSW	3	25,490,741 (GRCm39)	missense	probably damaging	1.00
R0010:Nlgn1	UTSW	3	25,490,006 (GRCm39)	splice site	probably benign
R0010:Nlgn1	UTSW	3	25,490,006 (GRCm39)	splice site	probably benign
R0123:Nlgn1	UTSW	3	25,490,089 (GRCm39)	missense	probably damaging	1.00
R0134:Nlgn1	UTSW	3	25,490,089 (GRCm39)	missense	probably damaging	1.00
R0294:Nlgn1	UTSW	3	26,187,625 (GRCm39)	missense	probably benign	0.23
R0798:Nlgn1	UTSW	3	25,488,410 (GRCm39)	missense	probably benign	0.05
R1051:Nlgn1	UTSW	3	25,966,869 (GRCm39)	missense	probably damaging	0.98
R1116:Nlgn1	UTSW	3	25,488,038 (GRCm39)	missense	probably benign	0.00
R1289:Nlgn1	UTSW	3	25,488,400 (GRCm39)	missense	possibly damaging	0.87
R1522:Nlgn1	UTSW	3	25,490,073 (GRCm39)	missense	probably damaging	1.00
R1550:Nlgn1	UTSW	3	25,966,808 (GRCm39)	missense	probably damaging	1.00
R1669:Nlgn1	UTSW	3	25,490,298 (GRCm39)	missense	probably damaging	1.00
R1853:Nlgn1	UTSW	3	26,187,671 (GRCm39)	missense	possibly damaging	0.80
R1856:Nlgn1	UTSW	3	25,494,201 (GRCm39)	nonsense	probably null
R1935:Nlgn1	UTSW	3	26,385,939 (GRCm39)	utr 5 prime	probably benign
R1936:Nlgn1	UTSW	3	26,385,939 (GRCm39)	utr 5 prime	probably benign
R1952:Nlgn1	UTSW	3	25,490,464 (GRCm39)	missense	probably damaging	1.00
R1953:Nlgn1	UTSW	3	25,490,464 (GRCm39)	missense	probably damaging	1.00
R2004:Nlgn1	UTSW	3	25,488,034 (GRCm39)	missense	probably benign	0.29
R2114:Nlgn1	UTSW	3	26,187,414 (GRCm39)	missense	probably damaging	1.00
R2116:Nlgn1	UTSW	3	26,187,414 (GRCm39)	missense	probably damaging	1.00
R2198:Nlgn1	UTSW	3	25,487,925 (GRCm39)	missense	probably damaging	0.99
R2994:Nlgn1	UTSW	3	25,490,162 (GRCm39)	missense	probably damaging	1.00
R4190:Nlgn1	UTSW	3	25,488,062 (GRCm39)	missense	probably benign
R4196:Nlgn1	UTSW	3	25,488,556 (GRCm39)	missense	probably damaging	1.00
R4613:Nlgn1	UTSW	3	25,490,186 (GRCm39)	missense	probably benign	0.01
R4654:Nlgn1	UTSW	3	26,187,850 (GRCm39)	missense	possibly damaging	0.51
R4757:Nlgn1	UTSW	3	25,490,507 (GRCm39)	missense	possibly damaging	0.63
R4757:Nlgn1	UTSW	3	25,490,332 (GRCm39)	missense	probably damaging	1.00
R4815:Nlgn1	UTSW	3	25,490,194 (GRCm39)	missense	probably damaging	0.99
R4884:Nlgn1	UTSW	3	25,966,838 (GRCm39)	missense	probably damaging	1.00
R4966:Nlgn1	UTSW	3	25,974,401 (GRCm39)	missense	possibly damaging	0.65
R5119:Nlgn1	UTSW	3	25,487,958 (GRCm39)	missense	probably damaging	0.99
R5842:Nlgn1	UTSW	3	26,187,892 (GRCm39)	splice site	probably null
R6218:Nlgn1	UTSW	3	25,490,257 (GRCm39)	missense	probably damaging	1.00
R6397:Nlgn1	UTSW	3	25,487,827 (GRCm39)	missense	possibly damaging	0.53
R6500:Nlgn1	UTSW	3	25,488,094 (GRCm39)	missense	possibly damaging	0.84
R6822:Nlgn1	UTSW	3	26,187,796 (GRCm39)	missense	probably benign	0.00
R6846:Nlgn1	UTSW	3	25,490,506 (GRCm39)	missense	probably damaging	0.99
R7047:Nlgn1	UTSW	3	25,490,199 (GRCm39)	nonsense	probably null
R7147:Nlgn1	UTSW	3	26,187,509 (GRCm39)	missense	probably benign	0.02
R7754:Nlgn1	UTSW	3	25,488,467 (GRCm39)	missense	probably damaging	1.00
R7886:Nlgn1	UTSW	3	25,490,071 (GRCm39)	missense	probably damaging	1.00
R8184:Nlgn1	UTSW	3	25,490,363 (GRCm39)	missense	probably damaging	1.00
R8261:Nlgn1	UTSW	3	25,487,816 (GRCm39)	missense	possibly damaging	0.53
R8304:Nlgn1	UTSW	3	26,187,534 (GRCm39)	missense	probably damaging	1.00
R8364:Nlgn1	UTSW	3	25,490,140 (GRCm39)	missense	probably benign	0.00
R8503:Nlgn1	UTSW	3	26,187,522 (GRCm39)	missense	probably damaging	0.99
R9035:Nlgn1	UTSW	3	25,488,595 (GRCm39)	missense	probably damaging	1.00
R9053:Nlgn1	UTSW	3	25,488,607 (GRCm39)	missense	probably damaging	1.00
R9209:Nlgn1	UTSW	3	25,966,804 (GRCm39)	critical splice donor site	probably null
R9268:Nlgn1	UTSW	3	25,490,548 (GRCm39)	missense	probably damaging	0.96
R9368:Nlgn1	UTSW	3	25,488,622 (GRCm39)	missense	probably damaging	0.99
R9492:Nlgn1	UTSW	3	25,488,480 (GRCm39)	nonsense	probably null
R9596:Nlgn1	UTSW	3	25,488,587 (GRCm39)	missense	probably damaging	1.00
R9647:Nlgn1	UTSW	3	25,488,182 (GRCm39)	missense	probably damaging	1.00
R9697:Nlgn1	UTSW	3	25,494,035 (GRCm39)	missense	possibly damaging	0.52
Z1176:Nlgn1	UTSW	3	25,490,768 (GRCm39)	missense	probably benign	0.12

Predicted Primers

PCR Primer
(F):5'- CTTCACGCAATTGGAATTTGC -3'
(R):5'- GAGTCCATCCATCCACATGAG -3'

Sequencing Primer
(F):5'- TTTCAAAACCCCCAAAGTTCTTG -3'
(R):5'- CACATGAGGTGGTTCTTCGGAC -3'

Posted On

2015-02-05