Mutagenetix > Incidental Mutation

Incidental Mutation 'R2004:Nlgn1'

223320

Institutional Source

Beutler Lab

Gene Symbol

Nlgn1

Ensembl Gene

ENSMUSG00000063887

Gene Name

neuroligin 1

Synonyms

NL1, Nlg1, 6330415N05Rik

MMRRC Submission

040013-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2004 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

25480379-26386609 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 25488034 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 738 (I738T)

Ref Sequence

ENSEMBL: ENSMUSP00000142086 (fasta)

Gene Model

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

AlphaFold

Q99K10

Predicted Effect

probably benign
Transcript: ENSMUST00000075054
AA Change: I767T

PolyPhen 2 Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000074565
Gene: ENSMUSG00000063887
AA Change: I767T

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: I738T

PolyPhen 2 Score 0.294 (Sensitivity: 0.91; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000103944
Gene: ENSMUSG00000063887
AA Change: I738T

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: I738T

PolyPhen 2 Score 0.294 (Sensitivity: 0.91; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000142086
Gene: ENSMUSG00000063887
AA Change: I738T

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: I767T

PolyPhen 2 Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887
AA Change: I767T

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: 94.9%

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: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aass	A	T	6: 23,092,561 (GRCm39)	Y146*	probably null	Het
Adcy2	A	G	13: 68,944,722 (GRCm39)	L220P	probably damaging	Het
Agl	T	C	3: 116,574,914 (GRCm39)	Y660C	probably damaging	Het
Ak1	A	G	2: 32,519,622 (GRCm39)	T17A	probably benign	Het
Amph	G	A	13: 19,326,198 (GRCm39)	V643M	probably damaging	Het
Ankrd11	A	T	8: 123,629,161 (GRCm39)		probably null	Het
Ap5b1	T	C	19: 5,620,502 (GRCm39)	S641P	possibly damaging	Het
Apoc4	A	G	7: 19,415,304 (GRCm39)	M1T	probably null	Het
Arhgap5	T	C	12: 52,564,817 (GRCm39)	V596A	probably benign	Het
Ascc3	A	G	10: 50,493,838 (GRCm39)	E91G	probably damaging	Het
Bach2	T	A	4: 32,580,055 (GRCm39)	V637E	probably benign	Het
Bicd2	T	G	13: 49,532,881 (GRCm39)	L489R	possibly damaging	Het
Bltp1	C	T	3: 36,949,527 (GRCm39)	T2I	possibly damaging	Het
Boc	A	T	16: 44,322,007 (GRCm39)		probably null	Het
Cbln2	T	A	18: 86,734,791 (GRCm39)	V188D	probably damaging	Het
Ccl11	A	C	11: 81,953,123 (GRCm39)	T94P	probably damaging	Het
Cd109	A	T	9: 78,611,044 (GRCm39)	H1220L	probably benign	Het
Cd226	A	G	18: 89,265,435 (GRCm39)	I125V	probably benign	Het
Cep135	T	A	5: 76,780,176 (GRCm39)		probably null	Het
Cgnl1	T	G	9: 71,537,821 (GRCm39)	E1233A	probably damaging	Het
Ckap5	T	A	2: 91,437,891 (GRCm39)	D1597E	possibly damaging	Het
Clptm1	A	G	7: 19,380,762 (GRCm39)	I63T	possibly damaging	Het
Cpsf7	C	T	19: 10,518,073 (GRCm39)	P428S	probably damaging	Het
Cuedc1	C	T	11: 88,068,216 (GRCm39)	P155S	probably damaging	Het
Dgkb	T	C	12: 38,134,228 (GRCm39)	Y45H	probably damaging	Het
Dglucy	T	C	12: 100,823,181 (GRCm39)	F459L	probably damaging	Het
Dmp1	T	A	5: 104,359,790 (GRCm39)	D155E	possibly damaging	Het
Dnah1	T	A	14: 31,023,813 (GRCm39)	I960F	possibly damaging	Het
Drosha	G	T	15: 12,915,467 (GRCm39)	M795I	probably damaging	Het
Dsg1b	A	G	18: 20,529,532 (GRCm39)	T326A	probably damaging	Het
Dusp16	T	G	6: 134,695,802 (GRCm39)	N343T	probably benign	Het
Faim2	T	C	15: 99,398,127 (GRCm39)	S274G	possibly damaging	Het
Fhip2a	G	T	19: 57,370,324 (GRCm39)	V523L	probably benign	Het
Fndc1	T	C	17: 8,023,761 (GRCm39)	R65G	probably damaging	Het
Fnip2	A	T	3: 79,419,632 (GRCm39)		probably benign	Het
Grm3	T	C	5: 9,639,793 (GRCm39)	Y84C	possibly damaging	Het
Herc2	T	C	7: 55,787,607 (GRCm39)	F1755L	probably damaging	Het
Hivep1	C	T	13: 42,313,625 (GRCm39)	T1955I	possibly damaging	Het
Ift20	T	C	11: 78,431,797 (GRCm39)	I97T	probably damaging	Het
Il36rn	T	C	2: 24,171,376 (GRCm39)	C155R	probably damaging	Het
Lca5l	T	A	16: 95,963,849 (GRCm39)	K358N	probably damaging	Het
Lca5l	T	C	16: 95,977,218 (GRCm39)	N196S	possibly damaging	Het
Maf1	G	A	15: 76,237,563 (GRCm39)	D175N	probably damaging	Het
Mical3	T	C	6: 120,928,283 (GRCm39)	K996E	probably damaging	Het
Midn	A	G	10: 79,990,983 (GRCm39)	N331S	probably benign	Het
Mki67	T	A	7: 135,300,238 (GRCm39)	K1599*	probably null	Het
Mlx	A	G	11: 100,979,805 (GRCm39)	Q162R	possibly damaging	Het
Nalf1	A	G	8: 9,820,607 (GRCm39)	S138P	probably benign	Het
Ngp	T	C	9: 110,249,929 (GRCm39)	C76R	probably damaging	Het
Nin	C	T	12: 70,072,251 (GRCm39)	G1210D	probably benign	Het
Nop53	A	C	7: 15,672,153 (GRCm39)	F465C	probably damaging	Het
Npas3	A	G	12: 54,114,680 (GRCm39)	D503G	possibly damaging	Het
Npbwr1	T	A	1: 5,986,570 (GRCm39)	S315C	probably damaging	Het
Nup42	G	T	5: 24,386,989 (GRCm39)	G260*	probably null	Het
Ogdh	G	C	11: 6,284,626 (GRCm39)	R200P	possibly damaging	Het
Or4b13	T	A	2: 90,083,036 (GRCm39)	I99L	probably benign	Het
Or52n20	A	G	7: 104,320,808 (GRCm39)	T300A	possibly damaging	Het
Or5m13b	T	G	2: 85,753,939 (GRCm39)		probably null	Het
Or6ae1	C	T	7: 139,742,729 (GRCm39)	V45I	probably damaging	Het
Or7g16	G	A	9: 18,726,801 (GRCm39)	S263L	probably benign	Het
Or7g33	A	T	9: 19,448,688 (GRCm39)	C179*	probably null	Het
Ovgp1	T	A	3: 105,894,309 (GRCm39)		probably benign	Het
Papln	T	A	12: 83,819,992 (GRCm39)	C150S	probably damaging	Het
Pde1c	A	T	6: 56,135,996 (GRCm39)	L316Q	probably damaging	Het
Pdlim2	C	T	14: 70,402,228 (GRCm39)	R296H	probably damaging	Het
Piezo2	G	T	18: 63,277,997 (GRCm39)	D302E	probably damaging	Het
Pirb	A	T	7: 3,720,637 (GRCm39)	L287Q	probably benign	Het
Plin1	A	G	7: 79,375,378 (GRCm39)		probably benign	Het
Plxnc1	A	G	10: 94,688,484 (GRCm39)	I698T	probably damaging	Het
Ppp1r12c	G	T	7: 4,485,974 (GRCm39)	C572*	probably null	Het
Ptgis	T	C	2: 167,056,769 (GRCm39)	M273V	possibly damaging	Het
Samd14	C	A	11: 94,914,110 (GRCm39)	T283K	probably damaging	Het
Scnn1g	A	T	7: 121,337,411 (GRCm39)	K91*	probably null	Het
Slc24a4	A	G	12: 102,180,166 (GRCm39)	Q95R	probably damaging	Het
Slfn9	T	G	11: 82,879,027 (GRCm39)	D34A	probably benign	Het
Smarca4	A	T	9: 21,588,776 (GRCm39)	I1193F	probably damaging	Het
Spata31e5	A	G	1: 28,816,260 (GRCm39)	W591R	probably damaging	Het
Sphkap	T	C	1: 83,255,632 (GRCm39)	M706V	probably benign	Het
Stard9	C	A	2: 120,504,117 (GRCm39)	S221R	probably damaging	Het
Stxbp1	T	C	2: 32,688,201 (GRCm39)	D488G	probably damaging	Het
Sugp2	C	T	8: 70,695,306 (GRCm39)		probably null	Het
Tekt5	T	C	16: 10,213,070 (GRCm39)	I72V	probably benign	Het
Themis	T	A	10: 28,658,720 (GRCm39)	N582K	probably benign	Het
Tmed11	C	A	5: 108,934,000 (GRCm39)	M65I	possibly damaging	Het
Top3a	G	T	11: 60,633,315 (GRCm39)	P927Q	probably damaging	Het
Trpa1	A	T	1: 14,976,207 (GRCm39)	N165K	possibly damaging	Het
Tsfm	A	G	10: 126,866,663 (GRCm39)	S2P	probably damaging	Het
Wdr47	C	A	3: 108,534,758 (GRCm39)	S559*	probably null	Het
Wnt2b	T	C	3: 104,860,331 (GRCm39)	Y192C	probably damaging	Het
Zfp280b	A	G	10: 75,874,370 (GRCm39)	D83G	probably benign	Het
Zfp345	T	C	2: 150,314,038 (GRCm39)	T500A	possibly damaging	Het
Zfp78	T	A	7: 6,382,074 (GRCm39)	C343S	probably damaging	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
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
R3056:Nlgn1	UTSW	3	25,487,860 (GRCm39)	missense	possibly damaging	0.53
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'- TCTGTCCTCCAGTAAATGTGTTG -3'
(R):5'- TCAGAGGGACTACTCCACAGAG -3'

Sequencing Primer
(F):5'- TGAATGTATGTAAGGGCTGAATCCC -3'
(R):5'- AGCTAAGTGTCACTATCGCAG -3'

Posted On

2014-08-25