Mutagenetix > Incidental Mutation

Incidental Mutation 'R4884:Nlgn1'

375498

Institutional Source

Beutler Lab

Gene Symbol

Nlgn1

Ensembl Gene

ENSMUSG00000063887

Gene Name

neuroligin 1

Synonyms

NL1, Nlg1, 6330415N05Rik

MMRRC Submission

041978-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4884 (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 25966838 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 205 (V205A)

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: V225A

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000074565
Gene: ENSMUSG00000063887
AA Change: V225A

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: V205A

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

SMART Domains

Protein: ENSMUSP00000103944
Gene: ENSMUSG00000063887
AA Change: V205A

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: V205A

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

SMART Domains

Protein: ENSMUSP00000142086
Gene: ENSMUSG00000063887
AA Change: V205A

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: V225A

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000142200
Gene: ENSMUSG00000063887
AA Change: V225A

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: 99.1%
3x: 98.4%
10x: 96.7%
20x: 93.5%

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: 113 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700049A03Rik	G	T	12: 71,211,320 (GRCm39)	E685*	probably null	Het
2700049A03Rik	A	T	12: 71,211,321 (GRCm39)	E685V	possibly damaging	Het
Aadat	C	T	8: 60,979,663 (GRCm39)	P175L	probably damaging	Het
Acot7	G	T	4: 152,270,664 (GRCm39)		probably benign	Het
Adad1	T	G	3: 37,130,813 (GRCm39)	F259V	possibly damaging	Het
Adora2a	A	G	10: 75,161,879 (GRCm39)	Y6C	probably null	Het
Ahnak	A	G	19: 8,990,118 (GRCm39)		probably benign	Het
Ankar	A	T	1: 72,737,966 (GRCm39)	M72K	probably damaging	Het
Ankrd45	A	G	1: 160,988,270 (GRCm39)	K176R	possibly damaging	Het
Ap3m2	T	C	8: 23,293,997 (GRCm39)	K18E	probably damaging	Het
Apol10b	C	T	15: 77,473,006 (GRCm39)	R16Q	possibly damaging	Het
Atp2b2	T	A	6: 113,819,147 (GRCm39)	T49S	possibly damaging	Het
B3gntl1	T	G	11: 121,520,795 (GRCm39)	Y206S	possibly damaging	Het
BC061237	G	A	14: 44,738,666 (GRCm39)	E22K	possibly damaging	Het
Bmp1	A	G	14: 70,712,655 (GRCm39)	V959A	probably benign	Het
Cep295	T	C	9: 15,263,056 (GRCm39)	E169G	probably damaging	Het
Cfap20dc	G	A	14: 8,578,394 (GRCm38)	T116I	probably damaging	Het
Cfap65	T	G	1: 74,942,283 (GRCm39)	E1757A	possibly damaging	Het
Cgrrf1	T	A	14: 47,090,912 (GRCm39)	I216N	possibly damaging	Het
Clstn2	T	A	9: 97,681,448 (GRCm39)	D64V	probably damaging	Het
Col27a1	T	A	4: 63,194,197 (GRCm39)	D851E	possibly damaging	Het
Coq9	C	T	8: 95,579,822 (GRCm39)	P259L	probably benign	Het
Cps1	A	G	1: 67,216,183 (GRCm39)	N836S	probably benign	Het
Cracd	A	T	5: 76,996,682 (GRCm39)	I47F	probably damaging	Het
Crebbp	T	C	16: 3,906,239 (GRCm39)	K1588E	probably damaging	Het
Cspg4	T	C	9: 56,805,353 (GRCm39)	W2055R	probably benign	Het
Cyp3a44	A	T	5: 145,714,792 (GRCm39)	M453K	probably damaging	Het
Dhx36	T	G	3: 62,391,681 (GRCm39)	D555A	probably damaging	Het
Dock2	A	T	11: 34,216,248 (GRCm39)	Y1219N	probably damaging	Het
Dpy19l2	A	T	9: 24,539,476 (GRCm39)	C492*	probably null	Het
Dusp22	A	G	13: 30,852,813 (GRCm39)	N16S	probably benign	Het
Epha1	A	G	6: 42,337,668 (GRCm39)	M805T	probably damaging	Het
Espl1	C	T	15: 102,232,505 (GRCm39)	A2071V	possibly damaging	Het
Fbxo11	T	A	17: 88,299,761 (GRCm39)	D863V	probably damaging	Het
Fbxo7	T	A	10: 85,865,014 (GRCm39)	Y106N	probably damaging	Het
Fhip1a	A	C	3: 85,590,918 (GRCm39)	C178G	probably damaging	Het
Fst	A	G	13: 114,590,920 (GRCm39)	V282A	probably damaging	Het
Gfra3	T	A	18: 34,844,304 (GRCm39)	M79L	probably benign	Het
Glp1r	T	C	17: 31,155,240 (GRCm39)	V409A	probably damaging	Het
Gm10799	T	A	2: 103,898,552 (GRCm39)	D51V	probably damaging	Het
Gm572	C	A	4: 148,751,819 (GRCm39)	T228N	possibly damaging	Het
Grip1	C	T	10: 119,911,211 (GRCm39)	T643M	probably damaging	Het
Hdgfl2	C	T	17: 56,403,265 (GRCm39)	R222C	possibly damaging	Het
Hecw2	T	A	1: 53,990,000 (GRCm39)	I125F	probably benign	Het
Hipk1	A	G	3: 103,651,338 (GRCm39)	S1153P	possibly damaging	Het
Insm2	T	C	12: 55,646,546 (GRCm39)	S97P	probably damaging	Het
Iqca1	A	G	1: 90,067,759 (GRCm39)	V164A	probably benign	Het
Kcna6	T	C	6: 126,715,689 (GRCm39)	D400G	probably benign	Het
Kctd1	T	C	18: 15,107,311 (GRCm39)	Y122C	probably damaging	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Klra2	T	C	6: 131,207,165 (GRCm39)	Y148C	probably damaging	Het
Krtap31-1	G	A	11: 99,799,310 (GRCm39)	C171Y	unknown	Het
Ldlrap1	C	T	4: 134,486,282 (GRCm39)	R59Q	probably benign	Het
Ltb	T	C	17: 35,414,234 (GRCm39)	I3T	probably benign	Het
Macf1	T	C	4: 123,348,802 (GRCm39)	I2477V	probably benign	Het
Mpdz	A	T	4: 81,279,713 (GRCm39)	I39N	probably damaging	Het
Mtcl3	A	T	10: 29,072,537 (GRCm39)	N610Y	probably damaging	Het
Mycbp2	A	G	14: 103,448,731 (GRCm39)	I1776T	probably damaging	Het
Myof	T	A	19: 37,930,805 (GRCm39)	E994V	probably damaging	Het
Myom3	A	G	4: 135,510,366 (GRCm39)	E553G	possibly damaging	Het
Mysm1	A	T	4: 94,847,185 (GRCm39)	C504S	probably damaging	Het
Nectin3	A	T	16: 46,269,249 (GRCm39)	H384Q	probably benign	Het
Net1	G	A	13: 3,934,252 (GRCm39)	R482*	probably null	Het
Nit1	T	C	1: 171,171,263 (GRCm39)	K193R	probably null	Het
Nr3c2	A	T	8: 77,635,438 (GRCm39)	I180F	possibly damaging	Het
Nup50l	A	T	6: 96,141,793 (GRCm39)	M417K	probably damaging	Het
Nup62	T	A	7: 44,478,289 (GRCm39)	S101R	probably damaging	Het
Or13c7	T	C	4: 43,854,890 (GRCm39)	S194P	probably damaging	Het
Or1l8	G	T	2: 36,818,024 (GRCm39)	T34K	possibly damaging	Het
Or4c3	A	G	2: 89,851,987 (GRCm39)	V141A	probably benign	Het
Or51b17	T	A	7: 103,542,862 (GRCm39)	I27F	probably benign	Het
Or56b2j	T	A	7: 104,353,068 (GRCm39)	I98N	probably damaging	Het
Or5b111	A	T	19: 13,291,034 (GRCm39)	I205N	probably benign	Het
Or5b124	A	T	19: 13,611,391 (GRCm39)	K305N	probably benign	Het
Or5p80	A	T	7: 108,229,819 (GRCm39)	I207F	probably damaging	Het
Osbpl6	A	T	2: 76,379,883 (GRCm39)	I158F	probably damaging	Het
Pcbp4	A	G	9: 106,339,301 (GRCm39)	T103A	probably benign	Het
Pcdha2	T	A	18: 37,073,953 (GRCm39)	L528Q	probably damaging	Het
Pcdhga5	T	C	18: 37,827,680 (GRCm39)	S43P	probably damaging	Het
Pdgfra	C	A	5: 75,349,973 (GRCm39)	N952K	probably benign	Het
Pla2r1	A	G	2: 60,365,328 (GRCm39)	S81P	probably damaging	Het
Rabggtb	A	T	3: 153,617,568 (GRCm39)	D43E	possibly damaging	Het
Rexo5	T	A	7: 119,424,774 (GRCm39)	C43*	probably null	Het
Robo1	T	A	16: 72,701,639 (GRCm39)	D168E	probably damaging	Het
Saxo4	A	T	19: 10,451,865 (GRCm39)	*428R	probably null	Het
Scimp	A	G	11: 70,688,865 (GRCm39)	M49T	unknown	Het
Sema3e	T	A	5: 14,275,579 (GRCm39)	V228E	probably damaging	Het
Sema6d	A	G	2: 124,498,738 (GRCm39)		probably null	Het
Serpinb6d	A	T	13: 33,850,428 (GRCm39)	D85V	possibly damaging	Het
Slc24a2	C	T	4: 86,909,745 (GRCm39)	V658I	probably damaging	Het
Snd1	T	C	6: 28,526,911 (GRCm39)	I198T	possibly damaging	Het
Snx33	C	T	9: 56,833,464 (GRCm39)	V202M	probably damaging	Het
Srcap	A	G	7: 127,121,189 (GRCm39)	E174G	probably damaging	Het
Srgap2	C	A	1: 131,220,314 (GRCm39)		probably null	Het
Stxbp5	A	T	10: 9,688,085 (GRCm39)	Y405*	probably null	Het
Thsd4	C	T	9: 59,895,320 (GRCm39)	R710H	probably benign	Het
Trp53inp1	T	A	4: 11,165,130 (GRCm39)	D51E	probably benign	Het
Ttc41	A	G	10: 86,566,882 (GRCm39)	D516G	probably benign	Het
Tut7	A	T	13: 59,937,266 (GRCm39)	L775H	probably damaging	Het
Uap1l1	A	G	2: 25,252,840 (GRCm39)	V400A	probably damaging	Het
Vit	T	C	17: 78,932,182 (GRCm39)	S430P	probably damaging	Het
Vmn1r9	T	A	6: 57,048,294 (GRCm39)	M123K	possibly damaging	Het
Vmn2r14	A	T	5: 109,369,384 (GRCm39)		probably null	Het
Vwa3a	A	G	7: 120,390,924 (GRCm39)	T746A	probably benign	Het
Wdfy4	G	T	14: 32,710,852 (GRCm39)	Y2578*	probably null	Het
Wdr53	A	T	16: 32,075,796 (GRCm39)	K334*	probably null	Het
Xpot	G	T	10: 121,442,713 (GRCm39)	H495Q	probably damaging	Het
Zfp109	T	C	7: 23,928,570 (GRCm39)	T288A	probably benign	Het
Zfp277	T	A	12: 40,413,152 (GRCm39)	E276V	probably damaging	Het
Zfp703	A	G	8: 27,468,729 (GRCm39)	D131G	probably benign	Het
Zfp985	T	A	4: 147,667,801 (GRCm39)	I223N	probably benign	Het
Zrsr2-ps1	T	C	11: 22,923,805 (GRCm39)	V193A	possibly damaging	Het
Zscan20	A	G	4: 128,481,958 (GRCm39)	I568T	possibly 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
R2004:Nlgn1	UTSW	3	25,488,034 (GRCm39)	missense	probably benign	0.29
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
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'- TTCCCAAGTTGCCATGACTCAG -3'
(R):5'- ATCATGCCCTCCTGTTCTTAAAATG -3'

Sequencing Primer
(F):5'- TTGCCATGACTCAGCAAGTG -3'
(R):5'- TGCACTGTTTCATTATGCATGTAG -3'

Posted On

2016-03-17