Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01533:Nlgn1'

89827

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Nlgn1

Ensembl Gene

ENSMUSG00000063887

Gene Name

neuroligin 1

Synonyms

NL1, Nlg1, 6330415N05Rik

Accession Numbers

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

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

IGL01533

Quality Score

Status

Chromosome

Chromosomal Location

25426215-26332460 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 25436363 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 400 (N400S)

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: N400S

PolyPhen 2 Score 0.692 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000074565
Gene: ENSMUSG00000063887
AA Change: N400S

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 benign
Transcript: ENSMUST00000108308
AA Change: N371S

PolyPhen 2 Score 0.034 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000103944
Gene: ENSMUSG00000063887
AA Change: N371S

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 benign
Transcript: ENSMUST00000191835
AA Change: N371S

PolyPhen 2 Score 0.034 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000142086
Gene: ENSMUSG00000063887
AA Change: N371S

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: N400S

PolyPhen 2 Score 0.692 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887
AA Change: N400S

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

Validation Efficiency

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: 41 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Afg3l2	C	A	18: 67,405,418	E757*	probably null	Het
Arhgap15	T	C	2: 44,243,153	V357A	probably damaging	Het
Asb13	T	C	13: 3,642,164	V48A	probably benign	Het
Bbs7	T	C	3: 36,610,235	R74G	possibly damaging	Het
Capn11	T	C	17: 45,632,904	H568R	probably benign	Het
Cbx5	T	C	15: 103,205,634	E61G	probably damaging	Het
Ccdc158	T	C	5: 92,609,956		probably null	Het
Col14a1	C	A	15: 55,420,840	N832K	unknown	Het
Cyp2a4	A	T	7: 26,308,544	K125N	probably damaging	Het
Dhx16	T	C	17: 35,882,047	L215P	probably damaging	Het
Dtx4	T	C	19: 12,478,215	M480V	possibly damaging	Het
Edaradd	A	G	13: 12,478,582		probably benign	Het
Galnt13	T	A	2: 54,880,132	M312K	probably damaging	Het
Gcdh	T	A	8: 84,889,362	R337W	probably damaging	Het
Gm28557	A	T	13: 67,071,332	C109*	probably null	Het
Gpr22	C	T	12: 31,708,710		probably benign	Het
Gria4	T	G	9: 4,502,395	L379F	probably damaging	Het
Gxylt2	T	C	6: 100,783,137	L211P	probably damaging	Het
Igsf10	T	A	3: 59,319,230	I2341F	probably damaging	Het
Macf1	T	C	4: 123,473,873	D2365G	probably damaging	Het
Morc2b	A	G	17: 33,135,721		probably benign	Het
Ncoa3	T	C	2: 166,055,025	S579P	probably benign	Het
Olfr1141	C	A	2: 87,753,068	R308S	probably benign	Het
Olfr146	C	T	9: 39,018,801	A247T	probably damaging	Het
Pi4ka	A	G	16: 17,308,201	S1102P	probably benign	Het
Polr1e	A	G	4: 45,019,328	Y59C	probably damaging	Het
Prex2	C	T	1: 11,186,741	Q1226*	probably null	Het
Rab12	A	T	17: 66,497,435	I176K	probably damaging	Het
Ryr2	A	T	13: 11,721,790	N2250K	probably damaging	Het
Sbf1	T	C	15: 89,288,716	T1865A	probably damaging	Het
Sema6b	G	A	17: 56,129,499		probably benign	Het
Smarcb1	C	T	10: 75,916,768		probably null	Het
Sos1	A	G	17: 80,415,082	L845S	probably damaging	Het
Stat4	T	A	1: 52,098,419	N456K	probably damaging	Het
Tex264	A	G	9: 106,673,599	I133T	probably benign	Het
Thoc1	T	C	18: 9,962,376	V87A	probably benign	Het
Tmem131	C	T	1: 36,818,722	D778N	probably damaging	Het
Tspan14	A	G	14: 40,916,819	I88T	probably benign	Het
Ttn	A	G	2: 76,951,941	S984P	probably damaging	Het
Ttn	C	A	2: 76,732,574	V28679L	possibly damaging	Het
Vangl1	T	C	3: 102,163,351	E423G	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
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
R7886:Nlgn1	UTSW	3	25435907	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

Posted On

2013-12-03