Mutagenetix > Incidental Mutation

Incidental Mutation 'R4613:Nlgn1'

350939

Institutional Source

Beutler Lab

Gene Symbol

Nlgn1

Ensembl Gene

ENSMUSG00000063887

Gene Name

neuroligin 1

Synonyms

NL1, Nlg1, 6330415N05Rik

MMRRC Submission

041824-MU

Accession Numbers

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

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4613 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

25426215-26332460 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 25436022 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 514 (T514A)

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 benign
Transcript: ENSMUST00000075054
AA Change: T514A

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000074565
Gene: ENSMUSG00000063887
AA Change: T514A

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: T485A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000103944
Gene: ENSMUSG00000063887
AA Change: T485A

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: T485A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000142086
Gene: ENSMUSG00000063887
AA Change: T485A

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: ENSMUST00000193603
AA Change: T514A

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887
AA Change: T514A

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: 99.4%
3x: 98.7%
10x: 97.4%
20x: 95.5%

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9830107B12Rik	A	T	17: 48,128,557	L130I	probably benign	Het
Abca9	A	G	11: 110,144,784	V670A	probably benign	Het
Adad1	A	G	3: 37,092,033	N517D	probably damaging	Het
Ankle2	T	C	5: 110,231,379	L48P	probably benign	Het
Aoc3	A	T	11: 101,337,659		probably benign	Het
Areg	A	G	5: 91,143,504	K102R	probably benign	Het
Bmp1	T	C	14: 70,508,523	T167A	probably damaging	Het
C4b	C	T	17: 34,734,551	G986D	probably benign	Het
Caml	G	T	13: 55,625,142	G200C	probably damaging	Het
Ccdc40	A	C	11: 119,231,532	R53S	probably benign	Het
Cdh22	T	A	2: 165,143,656	I337L	probably benign	Het
Col12a1	A	T	9: 79,647,601	V2065D	probably benign	Het
Copg2	A	G	6: 30,811,596	S591P	probably benign	Het
Cyp2d34	G	A	15: 82,616,325	P438S	probably damaging	Het
Dchs1	T	C	7: 105,772,724	D163G	probably damaging	Het
Depdc1b	T	C	13: 108,363,643	V230A	probably damaging	Het
Depdc5	T	A	5: 32,975,446	L1300H	probably damaging	Het
Dnah10	G	T	5: 124,762,869		probably null	Het
Dsc2	A	T	18: 20,041,819	D466E	probably damaging	Het
Dthd1	A	G	5: 62,827,068	D372G	probably damaging	Het
Eogt	G	T	6: 97,134,304	Q199K	probably benign	Het
Epha6	C	A	16: 59,666,597	R1029L	possibly damaging	Het
Eppin	C	A	2: 164,589,323	E128*	probably null	Het
Fam102b	A	T	3: 109,027,255	F23I	probably benign	Het
Fam160b1	C	A	19: 57,371,187	P53Q	probably damaging	Het
Fgf20	T	C	8: 40,286,611	R33G	probably benign	Het
Fgg	A	G	3: 83,010,090	N142S	probably damaging	Het
Gba	C	T	3: 89,208,644		probably null	Het
Gli2	A	G	1: 118,837,511	V970A	probably damaging	Het
Gramd1b	A	T	9: 40,307,993	V508D	probably damaging	Het
Gucy2c	T	A	6: 136,708,321	D898V	probably damaging	Het
Kcnj15	T	C	16: 95,295,794	Y92H	probably damaging	Het
L3mbtl3	A	T	10: 26,282,795	S652T	unknown	Het
Ldb2	G	T	5: 44,476,551	Q326K	probably benign	Het
Lipi	C	A	16: 75,560,801	R292L	probably benign	Het
Lrrc36	G	A	8: 105,449,614	V207I	possibly damaging	Het
Lyplal1	C	T	1: 186,088,752	G166D	probably benign	Het
Map1b	A	T	13: 99,430,302	Y1970*	probably null	Het
Map2	A	G	1: 66,425,469	N287D	probably damaging	Het
Map3k11	A	T	19: 5,697,470	Q578L	probably benign	Het
Map3k11	G	T	19: 5,697,471	Q578H	probably damaging	Het
Map4k4	G	A	1: 40,017,191	S1012N	probably benign	Het
Mapk13	A	T	17: 28,769,452	N15Y	probably damaging	Het
Mapk15	G	A	15: 75,995,910	A125T	probably damaging	Het
Mrgprb1	C	A	7: 48,447,708	R152L	possibly damaging	Het
Muc5ac	T	G	7: 141,791,103	Y104D	possibly damaging	Het
Myo1h	A	G	5: 114,348,379	N566S	possibly damaging	Het
Myo1h	C	A	5: 114,351,676	H647Q	probably benign	Het
Neo1	A	G	9: 58,889,041	I1201T	possibly damaging	Het
Olfr120	A	G	17: 37,726,696	Y224C	probably damaging	Het
Olfr533	A	T	7: 140,467,068	Y289F	probably damaging	Het
Olfr8	A	G	10: 78,956,065	N287D	probably damaging	Het
Olfr985	T	A	9: 40,127,722	K80*	probably null	Het
Orc2	A	T	1: 58,500,309	L57*	probably null	Het
Otoa	G	A	7: 121,145,568	V850M	probably damaging	Het
Pcnx3	T	C	19: 5,667,219	T1579A	possibly damaging	Het
Pde5a	A	T	3: 122,823,093	Y564F	probably damaging	Het
Pdxk	A	C	10: 78,447,919	I147S	probably damaging	Het
Pfdn5	A	G	15: 102,328,752	D108G	probably benign	Het
Pink1	T	C	4: 138,317,310	D342G	probably damaging	Het
Prkacb	A	T	3: 146,737,998	V336E	probably damaging	Het
Ptpro	C	A	6: 137,416,836	S13*	probably null	Het
Rfng	A	G	11: 120,782,650	L215P	probably damaging	Het
Rpn2	T	C	2: 157,302,425	F336L	possibly damaging	Het
Sacs	A	G	14: 61,211,797		probably null	Het
Sirpb1a	T	A	3: 15,417,037	Y77F	probably benign	Het
Skiv2l2	C	A	13: 112,921,739	E53*	probably null	Het
Slc30a8	A	G	15: 52,333,575	D294G	probably benign	Het
Sox13	T	C	1: 133,388,934	I212V	probably benign	Het
Srebf2	T	A	15: 82,185,348	I657N	possibly damaging	Het
Srsf6	C	A	2: 162,933,709	T146K	probably benign	Het
Strn4	T	C	7: 16,824,163	V162A	possibly damaging	Het
Sulf2	T	C	2: 166,132,605	D53G	probably damaging	Het
Tbc1d8	T	A	1: 39,372,708	I1016F	probably damaging	Het
Tfrc	G	T	16: 32,618,657	A278S	probably damaging	Het
Tnrc6a	T	G	7: 123,184,289		probably null	Het
Vmn1r83	T	C	7: 12,321,768	I121V	probably benign	Het
Vps13d	T	C	4: 145,131,655	S2200G	possibly damaging	Het
Washc2	T	A	6: 116,229,269	D397E	probably damaging	Het
Wipf3	T	C	6: 54,485,555	L250P	probably damaging	Het
Xirp1	A	G	9: 120,019,682	F45S	probably damaging	Het
Xpo5	A	G	17: 46,236,963	T910A	probably benign	Het
Zfp235	T	C	7: 24,141,676	Y507H	probably 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
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

Predicted Primers

PCR Primer
(F):5'- TAGGGCAGAGTACTTTCCTGAGG -3'
(R):5'- TATGGATATCCTGAAGGCAAAGATG -3'

Sequencing Primer
(F):5'- GCAGAGTACTTTCCTGAGGTACTTAC -3'
(R):5'- ACGGACCATCAATGGGTA -3'

Posted On

2015-10-08