Mutagenetix > Incidental Mutation

Incidental Mutation 'R7886:Nlgn1'

609046

Institutional Source

Beutler Lab

Gene Symbol

Nlgn1

Ensembl Gene

ENSMUSG00000063887

Gene Name

neuroligin 1

Synonyms

NL1, Nlg1, 6330415N05Rik

MMRRC Submission

Accession Numbers

Ncbi RefSeq: NM_138666.3; NM_001163387.1; MGI:2179435

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7886 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

25426215-26332460 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 25435907 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 552 (D552G)

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

probably damaging
Transcript: ENSMUST00000075054
AA Change: D552G

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

SMART Domains

Protein: ENSMUSP00000074565
Gene: ENSMUSG00000063887
AA Change: D552G

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

probably damaging
Transcript: ENSMUST00000108308
AA Change: D523G

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

SMART Domains

Protein: ENSMUSP00000103944
Gene: ENSMUSG00000063887
AA Change: D523G

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

probably damaging
Transcript: ENSMUST00000191835
AA Change: D523G

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

SMART Domains

Protein: ENSMUSP00000142086
Gene: ENSMUSG00000063887
AA Change: D523G

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

probably damaging
Transcript: ENSMUST00000193603
AA Change: D552G

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

SMART Domains

Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887
AA Change: D552G

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: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

100% (53/53)

MGI Phenotype

Strain: 3687638
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: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A730049H05Rik	T	G	6: 92,834,456	I130S	unknown	Het
Ano5	A	G	7: 51,570,393	H427R	probably benign	Het
Atad2	A	T	15: 58,126,136	V182E	probably damaging	Het
B4galnt1	T	C	10: 127,167,054	Y147H	probably damaging	Het
C1s2	T	C	6: 124,628,330	S349G	possibly damaging	Het
Ccdc51	G	T	9: 109,091,587	A181S	probably damaging	Het
Dcc	G	A	18: 71,954,868	Q100*	probably null	Het
Dchs2	A	T	3: 83,305,085	I2064F	probably damaging	Het
Depdc1a	G	A	3: 159,516,069	V217I	probably benign	Het
Dnajc7	A	T	11: 100,601,803	F31I	probably benign	Het
Eftud2	C	T	11: 102,840,108	R825H	probably damaging	Het
Fam184a	T	C	10: 53,675,160	E237G	probably damaging	Het
Fdx1l	A	T	9: 21,073,327		probably null	Het
Frem1	T	C	4: 83,016,406	D106G	possibly damaging	Het
Gabrg3	G	A	7: 56,724,481	R446W	probably damaging	Het
Gm42669	A	G	5: 107,508,706	E362G		Het
Hmcn1	A	T	1: 150,657,470	I3022N	possibly damaging	Het
Ifna2	C	A	4: 88,683,269	V171F	probably damaging	Het
Igsf10	T	C	3: 59,328,327	N1478D	probably benign	Het
Kcnc1	C	A	7: 46,427,621	D282E	probably damaging	Het
Klhdc2	G	A	12: 69,304,632		probably null	Het
Macrod2	G	A	2: 141,724,645	G188S	probably damaging	Het
Mapkbp1	T	C	2: 120,012,647	F186L	possibly damaging	Het
Mettl21a	T	C	1: 64,615,184	E58G	probably damaging	Het
Muc16	A	T	9: 18,585,982	C6625S	probably benign	Het
Naip5	A	T	13: 100,246,181	S7T	probably benign	Het
Nfs1	T	A	2: 156,142,061	D132V	unknown	Het
Numa1	C	T	7: 102,013,865	T2066I	probably benign	Het
Olfr1355	A	G	10: 78,879,823	Y217C	possibly damaging	Het
Olfr330	C	A	11: 58,529,054	V311L	probably benign	Het
Olfr370	T	C	8: 83,541,947	S268P	possibly damaging	Het
Olfr730	A	T	14: 50,186,564	Y219N	probably damaging	Het
Olfr847	A	T	9: 19,375,906		probably null	Het
Pde11a	C	T	2: 76,291,203	V345I	probably benign	Het
Pglyrp2	A	G	17: 32,418,761	S98P	possibly damaging	Het
Pik3c3	C	T	18: 30,319,588	Q643*	probably null	Het
Pold2	T	C	11: 5,872,714	Y402C	probably damaging	Het
Pom121	T	C	5: 135,381,994	T770A	unknown	Het
Pou4f1	A	T	14: 104,466,792	V68E	probably damaging	Het
Ppfia1	G	T	7: 144,519,283	Q265K	probably benign	Het
Pygl	A	G	12: 70,206,356		probably null	Het
Rdh19	A	G	10: 127,850,300	T94A	probably benign	Het
Scgb1b12	A	G	7: 32,334,497	T61A	probably damaging	Het
Sirpb1c	C	T	3: 15,832,202	A337T	probably benign	Het
Sltm	C	G	9: 70,586,673	P802R	possibly damaging	Het
Tbc1d23	T	C	16: 57,189,383	E381G	possibly damaging	Het
Tnik	A	G	3: 28,666,139	I1304V	probably damaging	Het
Tpmt	C	A	13: 47,040,162	G54C	probably damaging	Het
Usp25	A	T	16: 77,113,771	Q905L	probably damaging	Het
Vmn1r91	T	A	7: 20,101,565	N136K	probably benign	Het
Wdr70	C	T	15: 8,079,249	E138K	probably benign	Het
Wrb	T	A	16: 96,145,568	L31Q	possibly damaging	Het
Zbed3	A	G	13: 95,336,125	D19G	possibly damaging	Het
Zfp369	A	G	13: 65,292,054	K184R	possibly damaging	Het

Other mutations in Nlgn1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00510:Nlgn1	APN	3	25436490	missense	probably benign	0.02
IGL00543:Nlgn1	APN	3	25433781	missense	probably damaging	1.00
IGL00960:Nlgn1	APN	3	25912697	missense	probably damaging	1.00
IGL01533:Nlgn1	APN	3	25436363	missense	possibly damaging	0.69
IGL02146:Nlgn1	APN	3	25912682	missense	probably damaging	0.96
IGL02616:Nlgn1	APN	3	25434245	missense	probably damaging	0.99
IGL03342:Nlgn1	APN	3	26133262	missense	probably damaging	1.00
ligation	UTSW	3	25436035	nonsense	probably null
G1citation:Nlgn1	UTSW	3	26133647	missense	probably benign	0.00
P0018:Nlgn1	UTSW	3	25436577	missense	probably damaging	1.00
R0010:Nlgn1	UTSW	3	25435842	splice site	probably benign
R0010:Nlgn1	UTSW	3	25435842	splice site	probably benign
R0123:Nlgn1	UTSW	3	25435925	missense	probably damaging	1.00
R0134:Nlgn1	UTSW	3	25435925	missense	probably damaging	1.00
R0294:Nlgn1	UTSW	3	26133476	missense	probably benign	0.23
R0798:Nlgn1	UTSW	3	25434246	missense	probably benign	0.05
R1051:Nlgn1	UTSW	3	25912705	missense	probably damaging	0.98
R1116:Nlgn1	UTSW	3	25433874	missense	probably benign	0.00
R1289:Nlgn1	UTSW	3	25434236	missense	possibly damaging	0.87
R1522:Nlgn1	UTSW	3	25435909	missense	probably damaging	1.00
R1550:Nlgn1	UTSW	3	25912644	missense	probably damaging	1.00
R1669:Nlgn1	UTSW	3	25436134	missense	probably damaging	1.00
R1853:Nlgn1	UTSW	3	26133522	missense	possibly damaging	0.80
R1856:Nlgn1	UTSW	3	25440037	nonsense	probably null
R1935:Nlgn1	UTSW	3	26331790	utr 5 prime	probably benign
R1936:Nlgn1	UTSW	3	26331790	utr 5 prime	probably benign
R1952:Nlgn1	UTSW	3	25436300	missense	probably damaging	1.00
R1953:Nlgn1	UTSW	3	25436300	missense	probably damaging	1.00
R2004:Nlgn1	UTSW	3	25433870	missense	probably benign	0.29
R2114:Nlgn1	UTSW	3	26133265	missense	probably damaging	1.00
R2116:Nlgn1	UTSW	3	26133265	missense	probably damaging	1.00
R2198:Nlgn1	UTSW	3	25433761	missense	probably damaging	0.99
R2994:Nlgn1	UTSW	3	25435998	missense	probably damaging	1.00
R3056:Nlgn1	UTSW	3	25433696	missense	possibly damaging	0.53
R4190:Nlgn1	UTSW	3	25433898	missense	probably benign
R4196:Nlgn1	UTSW	3	25434392	missense	probably damaging	1.00
R4613:Nlgn1	UTSW	3	25436022	missense	probably benign	0.01
R4654:Nlgn1	UTSW	3	26133701	missense	possibly damaging	0.51
R4757:Nlgn1	UTSW	3	25436168	missense	probably damaging	1.00
R4757:Nlgn1	UTSW	3	25436343	missense	possibly damaging	0.63
R4815:Nlgn1	UTSW	3	25436030	missense	probably damaging	0.99
R4884:Nlgn1	UTSW	3	25912674	missense	probably damaging	1.00
R4966:Nlgn1	UTSW	3	25920237	missense	possibly damaging	0.65
R5119:Nlgn1	UTSW	3	25433794	missense	probably damaging	0.99
R5842:Nlgn1	UTSW	3	26133743	splice site	probably null
R6218:Nlgn1	UTSW	3	25436093	missense	probably damaging	1.00
R6397:Nlgn1	UTSW	3	25433663	missense	possibly damaging	0.53
R6500:Nlgn1	UTSW	3	25433930	missense	possibly damaging	0.84
R6822:Nlgn1	UTSW	3	26133647	missense	probably benign	0.00
R6846:Nlgn1	UTSW	3	25436342	missense	probably damaging	0.99
R7047:Nlgn1	UTSW	3	25436035	nonsense	probably null
R7147:Nlgn1	UTSW	3	26133360	missense	probably benign	0.02
R7754:Nlgn1	UTSW	3	25434303	missense	probably damaging	1.00
R8184:Nlgn1	UTSW	3	25436199	missense	probably damaging	1.00
R8261:Nlgn1	UTSW	3	25433652	missense	possibly damaging	0.53
R8304:Nlgn1	UTSW	3	26133385	missense	probably damaging	1.00
R8364:Nlgn1	UTSW	3	25435976	missense	probably benign	0.00
R8503:Nlgn1	UTSW	3	26133373	missense	probably damaging	0.99
R9035:Nlgn1	UTSW	3	25434431	missense	probably damaging	1.00
R9053:Nlgn1	UTSW	3	25434443	missense	probably damaging	1.00
R9209:Nlgn1	UTSW	3	25912640	critical splice donor site	probably null
R9268:Nlgn1	UTSW	3	25436384	missense	probably damaging	0.96
R9368:Nlgn1	UTSW	3	25434458	missense	probably damaging	0.99
R9492:Nlgn1	UTSW	3	25434316	nonsense	probably null
R9596:Nlgn1	UTSW	3	25434423	missense	probably damaging	1.00
R9647:Nlgn1	UTSW	3	25434018	missense	probably damaging	1.00
R9697:Nlgn1	UTSW	3	25439871	missense	possibly damaging	0.52
Z1176:Nlgn1	UTSW	3	25436604	missense	probably benign	0.12

Predicted Primers

PCR Primer
(F):5'- TCAAGAATGTTCAAAGCACTGGTTC -3'
(R):5'- GCAGACCTTCACTCGAACTTTGG -3'

Sequencing Primer
(F):5'- ACTGGTTCTATCCCCAATATCAGAG -3'
(R):5'- CGAACTTTGGCTCACCTACATAC -3'

Posted On

2019-12-20