Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02616:Nlgn1'

300674

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 #

IGL02616

Quality Score

Status

Chromosome

Chromosomal Location

25426215-26332460 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 25434245 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 613 (Y613C)

Ref Sequence

ENSEMBL: ENSMUSP00000142086 (fasta)

Gene Model

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

AlphaFold

Q99K10

Predicted Effect

probably damaging
Transcript: ENSMUST00000075054
AA Change: Y642C

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000074565
Gene: ENSMUSG00000063887
AA Change: Y642C

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: Y613C

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000103944
Gene: ENSMUSG00000063887
AA Change: Y613C

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: Y613C

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000142086
Gene: ENSMUSG00000063887
AA Change: Y613C

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: Y642C

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887
AA Change: Y642C

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: 48 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700003E16Rik	A	G	6: 83,161,662	R190G	probably benign	Het
4931406B18Rik	T	C	7: 43,501,013		probably null	Het
Adcy4	T	C	14: 55,783,514		probably null	Het
Ahnak	C	A	19: 9,005,627	P1425Q	probably benign	Het
Arih1	A	G	9: 59,412,476	V285A	probably benign	Het
Atp13a1	T	C	8: 69,805,313	V906A	probably benign	Het
Atp2a2	A	T	5: 122,461,684	I548N	probably benign	Het
C2cd5	A	T	6: 143,035,111	S643T	probably benign	Het
Calcoco1	T	C	15: 102,715,850	D210G	probably damaging	Het
Cep128	A	G	12: 91,296,258	I289T	probably benign	Het
Ces1c	C	T	8: 93,106,615	M407I	probably benign	Het
Cntln	T	G	4: 85,115,452		probably null	Het
Cypt12	T	A	3: 17,948,728	H88Q	possibly damaging	Het
Ddc	T	A	11: 11,880,645		probably benign	Het
Dnajb12	T	C	10: 59,892,863		probably null	Het
Gata2	A	G	6: 88,205,480	T477A	possibly damaging	Het
Gckr	A	G	5: 31,327,075	D619G	probably benign	Het
Gm5699	A	T	1: 30,998,351		noncoding transcript	Het
Gm8257	T	A	14: 44,655,226	S106C	probably damaging	Het
Gpr15	A	C	16: 58,718,204	L174R	probably damaging	Het
Hnrnph3	T	A	10: 63,019,485	H7L	possibly damaging	Het
Ide	A	T	19: 37,298,056	I518N	unknown	Het
Igdcc4	G	A	9: 65,133,078	G957D	probably damaging	Het
Igsf10	G	A	3: 59,318,606	P2549S	probably benign	Het
Kcnj9	A	G	1: 172,325,964	S198P	probably damaging	Het
Lclat1	T	C	17: 73,169,533	I45T	probably benign	Het
Met	T	C	6: 17,553,347	L1044S	probably damaging	Het
Msh4	T	C	3: 153,857,523	T739A	probably benign	Het
Ncam1	T	C	9: 49,508,688	E776G	probably benign	Het
Ndufv3	G	A	17: 31,527,669	V178M	probably damaging	Het
Nmbr	T	C	10: 14,760,687		probably benign	Het
Orc1	T	A	4: 108,595,479	W184R	probably benign	Het
Pde6b	T	C	5: 108,431,541	S850P	probably benign	Het
Pip5k1c	C	A	10: 81,317,321		probably null	Het
Pnpt1	T	C	11: 29,135,505		probably benign	Het
Pomt2	T	A	12: 87,124,862	H378L	probably damaging	Het
Sh3gl3	C	T	7: 82,285,018		probably benign	Het
Thsd7a	A	T	6: 12,408,985	N679K	probably damaging	Het
Tns2	T	C	15: 102,111,415	M572T	probably benign	Het
Twf2	C	T	9: 106,212,756	Q103*	probably null	Het
Uncx	T	C	5: 139,546,768	I196T	possibly damaging	Het
Urgcp	A	G	11: 5,717,400	S313P	probably damaging	Het
Vmn1r222	A	T	13: 23,232,141	C301S	possibly damaging	Het
Vmn2r111	T	A	17: 22,571,050	Q325L	possibly damaging	Het
Vps4a	C	T	8: 107,042,277	R236W	probably damaging	Het
Wdr19	T	A	5: 65,223,581	H344Q	probably damaging	Het
Wiz	A	T	17: 32,359,469	D356E	probably damaging	Het
Zc3h10	T	C	10: 128,544,882	E202G	probably benign	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
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

2015-04-16