Mutagenetix > Incidental Mutation

Incidental Mutation 'R1398:Nectin3'

160264

Institutional Source

Beutler Lab

Gene Symbol

Nectin3

Ensembl Gene

ENSMUSG00000022656

Gene Name

nectin cell adhesion molecule 3

Synonyms

2610301B19Rik, nectin-3, 3000002N23Rik, Pvrl3, 4921513D19Rik

MMRRC Submission

039460-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.269) question?

Stock #

R1398 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

46208069-46318888 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 46269119 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 428 (Y428H)

Ref Sequence

ENSEMBL: ENSMUSP00000023334 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000023334] [ENSMUST00000023335] [ENSMUST00000096052] [ENSMUST00000121245]

AlphaFold

Q9JLB9

Predicted Effect

possibly damaging
Transcript: ENSMUST00000023334
AA Change: Y428H

PolyPhen 2 Score 0.953 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000023334
Gene: ENSMUSG00000022656
AA Change: Y428H

Domain	Start	End	E-Value	Type
low complexity region	24	48	N/A	INTRINSIC
IG	63	167	5.04e-9	SMART
Pfam:C2-set_2	173	257	1.5e-19	PFAM
Pfam:Ig_3	284	342	3.1e-6	PFAM
low complexity region	358	367	N/A	INTRINSIC
transmembrane domain	404	426	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000023335

SMART Domains

Protein: ENSMUSP00000023335
Gene: ENSMUSG00000022656

Domain	Start	End	E-Value	Type
low complexity region	24	48	N/A	INTRINSIC
IG	63	167	5.04e-9	SMART
Pfam:C2-set_2	173	257	2.5e-19	PFAM
Pfam:Ig_2	281	355	1.3e-6	PFAM
transmembrane domain	368	390	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000096052

SMART Domains

Protein: ENSMUSP00000093757
Gene: ENSMUSG00000022656

Domain	Start	End	E-Value	Type
low complexity region	24	48	N/A	INTRINSIC
IG	63	167	5.04e-9	SMART
Pfam:C2-set_2	173	257	2e-19	PFAM
Pfam:Ig_2	281	355	1e-6	PFAM
transmembrane domain	368	390	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000121245

SMART Domains

Protein: ENSMUSP00000113146
Gene: ENSMUSG00000022656

Domain	Start	End	E-Value	Type
transmembrane domain	43	65	N/A	INTRINSIC

Meta Mutation Damage Score

0.0743

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 95.6%
20x: 90.7%

Validation Efficiency

96% (75/78)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the nectin family of proteins, which function as adhesion molecules at adherens junctions. This family member interacts with other nectin-like proteins and with afadin, a filamentous actin-binding protein involved in the regulation of directional motility, cell proliferation and survival. This gene plays a role in ocular development involving the ciliary body. Mutations in this gene are believed to result in congenital ocular defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
PHENOTYPE: Homozygous null mice exhibit male infertility and eye abnormalities including microphthalmia, absent vitreous body, abnormal ciliary body, retinal layers, and lenses. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca17	T	C	17: 24,547,511 (GRCm39)	K288E	probably damaging	Het
Aldh3a2	T	C	11: 61,147,562 (GRCm39)		probably null	Het
Anks1b	A	G	10: 89,885,891 (GRCm39)	T196A	probably damaging	Het
Anks6	T	A	4: 47,044,926 (GRCm39)	T327S	possibly damaging	Het
Bdh2	T	C	3: 135,001,057 (GRCm39)		probably benign	Het
C4b	T	A	17: 34,949,693 (GRCm39)		probably benign	Het
Cacna2d1	G	A	5: 16,562,764 (GRCm39)	V847I	possibly damaging	Het
Cadps	G	T	14: 12,449,822 (GRCm38)	T1129K	probably damaging	Het
Cdc45	A	G	16: 18,600,721 (GRCm39)		probably benign	Het
Cep63	A	T	9: 102,480,285 (GRCm39)		probably benign	Het
Chil4	T	A	3: 106,126,825 (GRCm39)		probably null	Het
Cnot11	A	G	1: 39,584,261 (GRCm39)	R478G	probably damaging	Het
Cyp2c67	A	G	19: 39,627,069 (GRCm39)	S254P	probably damaging	Het
Dnah11	T	A	12: 118,020,841 (GRCm39)	K87*	probably null	Het
Dpy19l2	T	A	9: 24,492,559 (GRCm39)		probably benign	Het
Dsc1	A	T	18: 20,221,393 (GRCm39)	I694N	probably damaging	Het
Ehd4	A	T	2: 119,958,081 (GRCm39)	I168K	probably benign	Het
Eif4e	A	T	3: 138,252,136 (GRCm39)	N25Y	probably damaging	Het
Elapor2	A	G	5: 9,430,297 (GRCm39)	Y69C	probably damaging	Het
Eme2	G	A	17: 25,111,892 (GRCm39)	S263F	probably damaging	Het
Fgfrl1	T	A	5: 108,854,147 (GRCm39)		probably benign	Het
Fhip2a	T	A	19: 57,361,358 (GRCm39)		probably benign	Het
Gm3159	T	A	14: 4,398,586 (GRCm38)	Y92*	probably null	Het
Gm4922	T	A	10: 18,659,496 (GRCm39)	S409C	possibly damaging	Het
Gmcl1	G	A	6: 86,691,244 (GRCm39)		probably benign	Het
Grsf1	A	G	5: 88,813,706 (GRCm39)	Y231H	probably benign	Het
Heatr4	T	A	12: 84,014,395 (GRCm39)	H614L	possibly damaging	Het
Hoxa13	C	G	6: 52,260,647 (GRCm38)		probably benign	Het
Hoxa13	G	C	6: 52,260,648 (GRCm38)		probably benign	Het
Isg20l2	C	A	3: 87,846,061 (GRCm39)	L325I	probably benign	Het
Kalrn	A	G	16: 34,033,190 (GRCm39)	Y879H	probably damaging	Het
Kcnk10	C	A	12: 98,402,485 (GRCm39)	W318L	probably damaging	Het
Kctd1	T	C	18: 15,195,654 (GRCm39)	E323G	possibly damaging	Het
Kif4	G	T	X: 99,732,703 (GRCm39)	A492S	probably benign	Het
Krtap4-1	T	C	11: 99,518,558 (GRCm39)	T151A	unknown	Het
Ldlr	A	T	9: 21,650,838 (GRCm39)	Q449L	probably benign	Het
Lepr	T	A	4: 101,649,216 (GRCm39)	D872E	probably damaging	Het
Lgals12	C	T	19: 7,581,322 (GRCm39)		probably benign	Het
Lrig3	C	T	10: 125,838,957 (GRCm39)	P488L	probably benign	Het
Lrrc4b	A	C	7: 44,111,876 (GRCm39)	I583L	probably benign	Het
Lyst	T	C	13: 13,915,121 (GRCm39)	S3272P	possibly damaging	Het
Marchf2	T	C	17: 33,915,096 (GRCm39)	H166R	probably damaging	Het
Mtbp	C	A	15: 55,440,933 (GRCm39)	Y373*	probably null	Het
Myh2	C	T	11: 67,076,113 (GRCm39)	H767Y	probably benign	Het
Ncam1	G	A	9: 49,428,889 (GRCm39)		probably benign	Het
Neb	T	A	2: 52,179,658 (GRCm39)	N1282Y	probably damaging	Het
Nrros	A	T	16: 31,961,962 (GRCm39)	I649N	probably damaging	Het
Nvl	A	T	1: 180,924,691 (GRCm39)		probably benign	Het
Or5p70	T	A	7: 107,994,708 (GRCm39)	V127E	probably damaging	Het
Pms1	A	T	1: 53,246,435 (GRCm39)	V368E	possibly damaging	Het
Polq	T	A	16: 36,882,857 (GRCm39)	S1674T	possibly damaging	Het
Ppp1r21	T	C	17: 88,850,307 (GRCm39)	V31A	probably damaging	Het
Rev3l	T	A	10: 39,697,579 (GRCm39)	V692E	probably benign	Het
Robo4	T	C	9: 37,319,372 (GRCm39)		probably null	Het
Rps6kc1	T	C	1: 190,532,212 (GRCm39)	I597V	probably damaging	Het
Rtel1	T	A	2: 180,977,658 (GRCm39)		probably null	Het
Scn9a	A	G	2: 66,314,930 (GRCm39)	M1587T	probably benign	Het
Sec31b	T	A	19: 44,512,104 (GRCm39)	I597F	probably benign	Het
Skint5	T	C	4: 113,636,268 (GRCm39)	N650S	unknown	Het
Slc22a28	G	T	19: 8,107,566 (GRCm39)	S167*	probably null	Het
Slfn1	T	A	11: 83,011,968 (GRCm39)	M28K	probably damaging	Het
Smc6	T	C	12: 11,321,880 (GRCm39)		probably benign	Het
Sox8	T	C	17: 25,786,857 (GRCm39)	H282R	probably benign	Het
Spata31e2	G	T	1: 26,724,422 (GRCm39)	Q253K	possibly damaging	Het
Syngr3	C	A	17: 24,905,414 (GRCm39)	V161L	probably benign	Het
Trak1	C	T	9: 121,283,425 (GRCm39)	S397F	probably damaging	Het
Uso1	C	T	5: 92,329,327 (GRCm39)	A405V	probably benign	Het
Uvrag	G	T	7: 98,715,027 (GRCm39)	Y190*	probably null	Het
Vps13d	A	T	4: 144,826,553 (GRCm39)	L1726Q	probably null	Het
Vwf	A	T	6: 125,580,420 (GRCm39)	Q556L	probably benign	Het
Wdr70	T	A	15: 8,065,325 (GRCm39)	M246L	probably benign	Het
Yipf3	T	C	17: 46,562,372 (GRCm39)	F285S	probably damaging	Het
Zdhhc13	G	A	7: 48,476,621 (GRCm39)	G579R	probably damaging	Het
Zdhhc18	G	C	4: 133,354,608 (GRCm39)	F125L	probably benign	Het

Other mutations in Nectin3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01456:Nectin3	APN	16	46,279,216 (GRCm39)	missense	probably benign	0.23
R0373:Nectin3	UTSW	16	46,278,550 (GRCm39)	missense	probably damaging	0.99
R0550:Nectin3	UTSW	16	46,279,183 (GRCm39)	missense	possibly damaging	0.86
R1219:Nectin3	UTSW	16	46,275,042 (GRCm39)	nonsense	probably null
R1251:Nectin3	UTSW	16	46,284,205 (GRCm39)	missense	possibly damaging	0.82
R1439:Nectin3	UTSW	16	46,268,757 (GRCm39)	nonsense	probably null
R2250:Nectin3	UTSW	16	46,275,099 (GRCm39)	missense	probably benign	0.00
R2448:Nectin3	UTSW	16	46,268,878 (GRCm39)	splice site	probably null
R2483:Nectin3	UTSW	16	46,215,542 (GRCm39)	missense	possibly damaging	0.83
R4523:Nectin3	UTSW	16	46,268,953 (GRCm39)	missense	probably benign	0.15
R4709:Nectin3	UTSW	16	46,284,306 (GRCm39)	missense	possibly damaging	0.58
R4809:Nectin3	UTSW	16	46,268,523 (GRCm39)	intron	probably benign
R4884:Nectin3	UTSW	16	46,269,249 (GRCm39)	missense	probably benign	0.01
R5051:Nectin3	UTSW	16	46,268,913 (GRCm39)	missense	possibly damaging	0.95
R5061:Nectin3	UTSW	16	46,268,812 (GRCm39)	missense	probably benign	0.03
R5272:Nectin3	UTSW	16	46,268,839 (GRCm39)	missense	possibly damaging	0.82
R5365:Nectin3	UTSW	16	46,284,469 (GRCm39)	nonsense	probably null
R5768:Nectin3	UTSW	16	46,279,180 (GRCm39)	missense	probably damaging	0.98
R5987:Nectin3	UTSW	16	46,284,508 (GRCm39)	missense	probably benign	0.00
R6029:Nectin3	UTSW	16	46,256,763 (GRCm39)	missense	probably benign	0.08
R6131:Nectin3	UTSW	16	46,215,515 (GRCm39)	missense	probably damaging	0.98
R6251:Nectin3	UTSW	16	46,215,513 (GRCm39)	missense	probably damaging	0.99
R6299:Nectin3	UTSW	16	46,284,345 (GRCm39)	missense	probably damaging	0.98
R6347:Nectin3	UTSW	16	46,278,487 (GRCm39)	missense	probably benign	0.01
R6360:Nectin3	UTSW	16	46,231,472 (GRCm39)	missense	probably benign	0.09
R6505:Nectin3	UTSW	16	46,269,184 (GRCm39)	missense	possibly damaging	0.68
R6703:Nectin3	UTSW	16	46,284,205 (GRCm39)	missense	probably damaging	0.99
R6869:Nectin3	UTSW	16	46,215,506 (GRCm39)	missense	probably damaging	0.96
R7184:Nectin3	UTSW	16	46,215,484 (GRCm39)	missense	possibly damaging	0.66
R7298:Nectin3	UTSW	16	46,268,759 (GRCm39)	missense	probably damaging	1.00
R7455:Nectin3	UTSW	16	46,317,105 (GRCm39)	nonsense	probably null
R7973:Nectin3	UTSW	16	46,216,484 (GRCm39)	missense	probably benign	0.13
R7993:Nectin3	UTSW	16	46,279,184 (GRCm39)	missense	probably benign	0.01
R8108:Nectin3	UTSW	16	46,284,484 (GRCm39)	missense	possibly damaging	0.84
R8259:Nectin3	UTSW	16	46,256,754 (GRCm39)	missense	probably benign	0.00
R8511:Nectin3	UTSW	16	46,284,363 (GRCm39)	missense	probably damaging	1.00
R8971:Nectin3	UTSW	16	46,269,265 (GRCm39)	missense	probably benign
R9195:Nectin3	UTSW	16	46,279,259 (GRCm39)	nonsense	probably null
R9264:Nectin3	UTSW	16	46,274,998 (GRCm39)	missense	probably damaging	1.00
R9492:Nectin3	UTSW	16	46,215,511 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- CCTCCTGGAAATTACGGAGCCATC -3'
(R):5'- GACAGTTCAGTGGCATTCCTCACC -3'

Sequencing Primer
(F):5'- TTACGGAGCCATCTACATGAG -3'
(R):5'- GGCATTCCTCACCTGCTG -3'

Posted On

2014-03-14