Mutagenetix > Incidental Mutation

Incidental Mutation 'R4709:Nectin3'

355511

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

042018-MU

Accession Numbers

Essential gene?

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

Stock #

R4709 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

46208069-46318888 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 46284306 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Phenylalanine at position 126 (Y126F)

Ref Sequence

ENSEMBL: ENSMUSP00000093757 (fasta)

Gene Model

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

AlphaFold

Q9JLB9

Predicted Effect

possibly damaging
Transcript: ENSMUST00000023334
AA Change: Y126F

PolyPhen 2 Score 0.577 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000023334
Gene: ENSMUSG00000022656
AA Change: Y126F

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

possibly damaging
Transcript: ENSMUST00000023335
AA Change: Y126F

PolyPhen 2 Score 0.577 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000023335
Gene: ENSMUSG00000022656
AA Change: Y126F

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

possibly damaging
Transcript: ENSMUST00000096052
AA Change: Y126F

PolyPhen 2 Score 0.577 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000093757
Gene: ENSMUSG00000022656
AA Change: Y126F

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

noncoding transcript
Transcript: ENSMUST00000133935

Predicted Effect

unknown
Transcript: ENSMUST00000149901
AA Change: Y125F

SMART Domains

Protein: ENSMUSP00000117479
Gene: ENSMUSG00000022656
AA Change: Y125F

Domain	Start	End	E-Value	Type
low complexity region	24	48	N/A	INTRINSIC
IG	63	167	5.04e-9	SMART
Pfam:Ig_3	184	243	4.8e-5	PFAM

Meta Mutation Damage Score

0.0667

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.7%
20x: 93.9%

Validation Efficiency

97% (77/79)

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcf1	G	A	17: 36,271,069 (GRCm39)	T463M	probably damaging	Het
Arhgap35	C	T	7: 16,297,511 (GRCm39)	G518D	probably damaging	Het
Arhgdia	A	G	11: 120,470,517 (GRCm39)	Y110H	probably damaging	Het
Atp8b3	T	C	10: 80,372,604 (GRCm39)		probably null	Het
Bpifb6	T	A	2: 153,750,436 (GRCm39)	I309N	possibly damaging	Het
Cbr4	T	C	8: 61,943,061 (GRCm39)	V77A	possibly damaging	Het
Cers2	A	G	3: 95,227,534 (GRCm39)	Y54C	possibly damaging	Het
Cnbp	A	T	6: 87,821,120 (GRCm39)	H145Q	probably damaging	Het
Csmd1	A	T	8: 16,073,905 (GRCm39)	I2030N	possibly damaging	Het
Csmd1	A	G	8: 16,760,522 (GRCm39)		probably null	Het
Dhodh	T	C	8: 110,328,170 (GRCm39)		probably null	Het
Dnah11	T	A	12: 117,982,495 (GRCm39)	Y2558F	probably benign	Het
Dysf	C	A	6: 84,074,697 (GRCm39)	D499E	probably damaging	Het
En1	A	T	1: 120,534,872 (GRCm39)	Y387F	unknown	Het
Ephb2	C	A	4: 136,423,363 (GRCm39)	C305F	probably damaging	Het
Fryl	A	G	5: 73,238,315 (GRCm39)	V1477A	probably benign	Het
Gimap3	A	T	6: 48,742,327 (GRCm39)	L201Q	probably benign	Het
Gm10801	T	G	2: 98,494,246 (GRCm39)		probably null	Het
Grhl1	A	G	12: 24,636,132 (GRCm39)	I283V	possibly damaging	Het
Grid2ip	T	A	5: 143,374,658 (GRCm39)	L926H	probably damaging	Het
Gtf2h2	G	T	13: 100,605,523 (GRCm39)	C82*	probably null	Het
Gtf2ird1	T	C	5: 134,433,588 (GRCm39)	T280A	probably benign	Het
Gzmd	T	C	14: 56,367,698 (GRCm39)	I192V	probably null	Het
Hectd1	A	G	12: 51,834,695 (GRCm39)	V855A	possibly damaging	Het
Hey1	A	G	3: 8,730,963 (GRCm39)		probably benign	Het
Hpx	A	G	7: 105,249,243 (GRCm39)	S19P	probably benign	Het
Incenp	G	A	19: 9,853,964 (GRCm39)	R696W	unknown	Het
Itgam	T	C	7: 127,700,709 (GRCm39)	V493A	probably damaging	Het
Ldlrad3	A	G	2: 101,900,343 (GRCm39)	I53T	probably damaging	Het
Map3k7	G	T	4: 31,985,700 (GRCm39)	E208*	probably null	Het
Myh9	A	T	15: 77,671,717 (GRCm39)	I458N	probably damaging	Het
Myo1c	C	T	11: 75,560,856 (GRCm39)	R770*	probably null	Het
Nek5	A	T	8: 22,573,443 (GRCm39)	N504K	probably damaging	Het
Nlrp4c	T	A	7: 6,068,424 (GRCm39)	H108Q	probably benign	Het
Or10d5	A	T	9: 39,861,165 (GRCm39)	L301M	probably damaging	Het
Or2ak4	T	C	11: 58,649,013 (GRCm39)	V174A	possibly damaging	Het
Or2at1	A	T	7: 99,416,989 (GRCm39)	I207F	probably damaging	Het
Or5h17	A	T	16: 58,820,458 (GRCm39)	T137S	probably benign	Het
Or9a2	G	T	6: 41,748,442 (GRCm39)	Q264K	probably benign	Het
Or9i14	T	A	19: 13,792,814 (GRCm39)	I47F	possibly damaging	Het
Parp6	T	C	9: 59,549,052 (GRCm39)	I507T	probably damaging	Het
Pcdhb12	A	G	18: 37,570,548 (GRCm39)	T565A	probably benign	Het
Pclo	A	G	5: 14,828,572 (GRCm39)	N4676D	unknown	Het
Pdlim1	T	A	19: 40,211,180 (GRCm39)	H278L	probably benign	Het
Pfkfb3	G	A	2: 11,498,719 (GRCm39)	T46M	probably damaging	Het
Plscr2	A	G	9: 92,173,067 (GRCm39)	Y203C	probably damaging	Het
Plxna1	T	C	6: 89,311,733 (GRCm39)	D924G	possibly damaging	Het
Postn	T	A	3: 54,292,031 (GRCm39)		probably benign	Het
Ptpn23	A	G	9: 110,217,924 (GRCm39)	S674P	possibly damaging	Het
Ranbp6	C	T	19: 29,788,984 (GRCm39)	R456Q	probably benign	Het
Rbm43	A	T	2: 51,819,728 (GRCm39)	V46E	probably damaging	Het
Rlig1	T	C	10: 100,414,243 (GRCm39)	I139V	probably benign	Het
Rtn4r	A	G	16: 17,969,046 (GRCm39)	Y158C	probably damaging	Het
Ryr2	A	G	13: 11,731,884 (GRCm39)	I2352T	probably damaging	Het
Sbk2	G	T	7: 4,960,577 (GRCm39)	R198S	possibly damaging	Het
Scube3	G	A	17: 28,386,166 (GRCm39)		probably null	Het
Slc45a1	G	A	4: 150,722,697 (GRCm39)	P396S	probably benign	Het
Slc4a10	A	G	2: 62,087,861 (GRCm39)	D418G	probably null	Het
Smarcad1	A	G	6: 65,052,099 (GRCm39)	T411A	probably benign	Het
Smtn	G	A	11: 3,474,663 (GRCm39)	S716F	probably damaging	Het
Stag1	G	T	9: 100,620,092 (GRCm39)	R65L	probably damaging	Het
Stat1	A	T	1: 52,165,680 (GRCm39)	D92V	probably damaging	Het
Ttn	A	G	2: 76,582,428 (GRCm39)	Y22822H	probably damaging	Het
Vmn1r172	A	G	7: 23,359,606 (GRCm39)	T164A	probably benign	Het
Vmn2r118	A	T	17: 55,917,860 (GRCm39)	D217E	probably damaging	Het
Vmn2r26	A	G	6: 124,030,924 (GRCm39)	E553G	probably damaging	Het
Vmn2r96	T	C	17: 18,803,088 (GRCm39)	F333L	probably benign	Het
Ypel5	G	A	17: 73,155,726 (GRCm39)	R98H	probably benign	Het
Zfp719	C	T	7: 43,239,656 (GRCm39)	H415Y	probably damaging	Het
Zyg11a	T	C	4: 108,062,268 (GRCm39)	S176G	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
R1398:Nectin3	UTSW	16	46,269,119 (GRCm39)	missense	possibly damaging	0.95
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
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'- AGAGCCTAGACATACACAGCTTTAAG -3'
(R):5'- CAGTGTGGGGAAAGAATGTTTC -3'

Sequencing Primer
(F):5'- CATACACAGCTTTAAGACAGAATTTG -3'
(R):5'- TGTGGGGAAAGAATGTTTCATTGAAG -3'

Posted On

2015-10-21