Mutagenetix > Incidental Mutation

Incidental Mutation 'R7732:Nectin4'

595882

Institutional Source

Beutler Lab

Gene Symbol

Nectin4

Ensembl Gene

ENSMUSG00000006411

Gene Name

nectin cell adhesion molecule 4

Synonyms

Pvrl4, 1200017F15Rik, nectin 4, Prr4

MMRRC Submission

045788-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.079) question?

Stock #

R7732 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

171197741-171215855 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 171214246 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Valine at position 467 (E467V)

Ref Sequence

ENSEMBL: ENSMUSP00000006578 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000006578] [ENSMUST00000056449] [ENSMUST00000094325] [ENSMUST00000111286]

AlphaFold

Q8R007

Predicted Effect

probably benign
Transcript: ENSMUST00000006578
AA Change: E467V

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000006578
Gene: ENSMUSG00000006411
AA Change: E467V

Domain	Start	End	E-Value	Type
IG	36	145	9.26e-8	SMART
Pfam:Ig_2	147	241	4e-4	PFAM
Pfam:C2-set_2	150	233	9e-17	PFAM
IGc2	259	321	9.78e-7	SMART
transmembrane domain	348	370	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000056449

SMART Domains

Protein: ENSMUSP00000059389
Gene: ENSMUSG00000048865

Domain	Start	End	E-Value	Type
low complexity region	6	14	N/A	INTRINSIC
RhoGAP	31	212	1.4e-61	SMART
Blast:RhoGAP	225	285	2e-24	BLAST
low complexity region	348	366	N/A	INTRINSIC
low complexity region	367	378	N/A	INTRINSIC
low complexity region	452	463	N/A	INTRINSIC
low complexity region	498	510	N/A	INTRINSIC
low complexity region	514	534	N/A	INTRINSIC
low complexity region	667	690	N/A	INTRINSIC
low complexity region	736	752	N/A	INTRINSIC
low complexity region	924	940	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000094325
AA Change: E442V

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000091883
Gene: ENSMUSG00000006411
AA Change: E442V

Domain	Start	End	E-Value	Type
IG	36	145	9.26e-8	SMART
Pfam:Ig_2	147	241	2.1e-4	PFAM
Pfam:C2-set_2	150	233	8.7e-17	PFAM
IGc2	259	321	9.78e-7	SMART
transmembrane domain	348	370	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000111286
AA Change: E467V

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000106917
Gene: ENSMUSG00000006411
AA Change: E467V

Domain	Start	End	E-Value	Type
IG	100	209	9.26e-8	SMART
Pfam:C2-set_2	214	297	1.2e-16	PFAM
IGc2	323	385	9.78e-7	SMART
transmembrane domain	412	434	N/A	INTRINSIC

Meta Mutation Damage Score

0.0795

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.9%

Validation Efficiency

100% (73/73)

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. The encoded protein contains two immunoglobulin-like (Ig-like) C2-type domains and one Ig-like V-type domain. It is involved in cell adhesion through trans-homophilic and -heterophilic interactions. It is a single-pass type I membrane protein. The soluble form is produced by proteolytic cleavage at the cell surface by the metalloproteinase ADAM17/TACE. The secreted form is found in both breast tumor cell lines and breast tumor patients. Mutations in this gene are the cause of ectodermal dysplasia-syndactyly syndrome type 1, an autosomal recessive disorder. Alternatively spliced transcript variants have been found but the full-length nature of the variant has not been determined.[provided by RefSeq, Jan 2011]

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcd2	A	T	15: 91,075,451 (GRCm39)	S121T	possibly damaging	Het
Alpk1	T	C	3: 127,478,041 (GRCm39)	M69V		Het
Ap3m2	G	T	8: 23,287,105 (GRCm39)	D192E	probably benign	Het
Arel1	A	G	12: 84,974,663 (GRCm39)	V493A	probably benign	Het
Arhgap27	T	C	11: 103,230,869 (GRCm39)	H140R	probably benign	Het
Bcat2	C	T	7: 45,234,617 (GRCm39)	T166M	possibly damaging	Het
Brd4	C	A	17: 32,440,386 (GRCm39)	A318S	unknown	Het
Cabp4	T	A	19: 4,185,994 (GRCm39)	T270S	probably benign	Het
Cd22	G	A	7: 30,569,482 (GRCm39)	R545C	probably damaging	Het
Cdc23	C	A	18: 34,769,755 (GRCm39)		probably null	Het
Chst4	G	A	8: 110,756,514 (GRCm39)	Q450*	probably null	Het
Ctsc	G	A	7: 87,946,367 (GRCm39)	R132Q	probably damaging	Het
Cyp2b19	A	G	7: 26,470,769 (GRCm39)	D470G	possibly damaging	Het
Dcc	C	T	18: 71,579,506 (GRCm39)	G689D	probably benign	Het
Disc1	G	T	8: 125,977,714 (GRCm39)	G779*	probably null	Het
Dock1	T	G	7: 134,346,699 (GRCm39)	D210E	probably benign	Het
Dynlt1a	A	G	17: 6,365,220 (GRCm39)	V14A	probably benign	Het
Dynlt2a3	A	G	17: 15,187,947 (GRCm39)	V109A	probably benign	Het
Epha10	A	G	4: 124,809,092 (GRCm39)	D779G		Het
Eprs1	A	G	1: 185,105,136 (GRCm39)	H137R	probably benign	Het
Eps15l1	A	C	8: 73,134,820 (GRCm39)	L447R	probably damaging	Het
Esyt1	A	G	10: 128,357,694 (GRCm39)		probably null	Het
Fam221a	A	G	6: 49,349,563 (GRCm39)	K43E	probably benign	Het
Fanci	A	G	7: 79,062,400 (GRCm39)	S309G	possibly damaging	Het
Fbxo48	T	A	11: 16,903,601 (GRCm39)	W76R	probably damaging	Het
Fgd4	A	G	16: 16,302,459 (GRCm39)	V32A	probably benign	Het
Foxe1	A	T	4: 46,345,287 (GRCm39)	D365V	unknown	Het
Gabrd	C	T	4: 155,470,075 (GRCm39)	R378H	probably benign	Het
Greb1	A	G	12: 16,723,864 (GRCm39)	S1862P	probably damaging	Het
H2al2b	T	C	Y: 2,720,436 (GRCm39)	H80R	possibly damaging	Het
Hectd4	T	C	5: 121,474,692 (GRCm39)	V2771A	probably benign	Het
Hoxa11	A	T	6: 52,220,415 (GRCm39)	F289L	probably damaging	Het
Hsp90aa1	A	G	12: 110,659,852 (GRCm39)	V412A	probably damaging	Het
Igsf11	A	G	16: 38,829,160 (GRCm39)	Q77R	probably damaging	Het
Lrig1	C	A	6: 94,603,358 (GRCm39)	M263I	probably benign	Het
Ms4a14	C	T	19: 11,279,047 (GRCm39)	M1170I	probably benign	Het
Ndufs7	G	A	10: 80,089,618 (GRCm39)		probably null	Het
Or8d1b	A	G	9: 38,887,560 (GRCm39)	E196G	probably damaging	Het
Otogl	G	A	10: 107,642,525 (GRCm39)	H1302Y	probably benign	Het
Pigg	A	G	5: 108,466,841 (GRCm39)	S241G	probably benign	Het
Pip4p1	C	T	14: 51,168,090 (GRCm39)	G48D	possibly damaging	Het
Pom121l12	T	A	11: 14,549,843 (GRCm39)	V183D	probably damaging	Het
Prickle2	T	A	6: 92,388,205 (GRCm39)	E455V	probably damaging	Het
Ptpn4	A	C	1: 119,620,532 (GRCm39)	V488G	probably benign	Het
Ranbp10	A	G	8: 106,499,723 (GRCm39)	I502T	probably benign	Het
Raph1	T	A	1: 60,572,447 (GRCm39)	Q40L	possibly damaging	Het
Rgs22	A	T	15: 36,026,127 (GRCm39)	C1056S	probably damaging	Het
Serpinb6b	G	A	13: 33,152,590 (GRCm39)	S33N	probably damaging	Het
Serpinb6d	A	G	13: 33,853,082 (GRCm39)	N158S	probably benign	Het
Serping1	A	T	2: 84,600,448 (GRCm39)	V298D	probably damaging	Het
Sgsm1	T	A	5: 113,414,196 (GRCm39)	H637L	probably benign	Het
Sh3rf2	G	T	18: 42,234,753 (GRCm39)	V179L	probably damaging	Het
Slc1a3	T	C	15: 8,680,472 (GRCm39)	T129A	probably benign	Het
Slit1	T	A	19: 41,592,847 (GRCm39)	Y1202F	probably benign	Het
Spsb2	T	C	6: 124,786,656 (GRCm39)	S130P	probably damaging	Het
Sulf1	A	G	1: 12,913,013 (GRCm39)	D749G	probably benign	Het
Taok3	A	G	5: 117,331,813 (GRCm39)	E10G	possibly damaging	Het
Tbl3	G	T	17: 24,923,136 (GRCm39)	A368D	probably benign	Het
Tdh	T	A	14: 63,733,507 (GRCm39)	H127L	probably damaging	Het
Tmem205	C	A	9: 21,838,703 (GRCm39)		probably null	Het
Tmem30a	A	C	9: 79,687,826 (GRCm39)	F114L	possibly damaging	Het
Tmprss15	T	C	16: 78,800,308 (GRCm39)	K607E	probably benign	Het
Tnxb	A	T	17: 34,913,254 (GRCm39)	D1756V	probably damaging	Het
Trhde	A	G	10: 114,623,969 (GRCm39)	F312L	probably benign	Het
Ttn	G	A	2: 76,656,793 (GRCm39)	P12494L	probably null	Het
Vmn2r61	A	G	7: 41,916,097 (GRCm39)	R237G	probably benign	Het
Vps13c	A	T	9: 67,847,798 (GRCm39)	N2187Y	probably damaging	Het
Wdr64	A	G	1: 175,617,495 (GRCm39)	T692A	probably benign	Het
Whamm	A	G	7: 81,221,172 (GRCm39)	N35D	probably damaging	Het
Wnt2	T	C	6: 18,023,335 (GRCm39)	S105G	probably damaging	Het
Zfp108	T	A	7: 23,960,952 (GRCm39)	H514Q	probably benign	Het
Zftraf1	C	T	15: 76,532,386 (GRCm39)	D241N	probably benign	Het
Znfx1	T	C	2: 166,884,589 (GRCm39)	K888E	possibly damaging	Het
Zzz3	T	C	3: 152,154,479 (GRCm39)	Y577H	probably damaging	Het

Other mutations in Nectin4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00819:Nectin4	APN	1	171,212,254 (GRCm39)	missense	probably damaging	1.00
IGL01558:Nectin4	APN	1	171,212,257 (GRCm39)	missense	probably benign	0.00
IGL02608:Nectin4	APN	1	171,212,341 (GRCm39)	missense	probably benign	0.05
R2047:Nectin4	UTSW	1	171,212,720 (GRCm39)	missense	possibly damaging	0.61
R2203:Nectin4	UTSW	1	171,213,797 (GRCm39)	missense	possibly damaging	0.78
R2518:Nectin4	UTSW	1	171,207,776 (GRCm39)	missense	probably benign	0.00
R4125:Nectin4	UTSW	1	171,213,301 (GRCm39)	missense	probably benign	0.02
R4708:Nectin4	UTSW	1	171,212,714 (GRCm39)	missense	probably benign	0.02
R4856:Nectin4	UTSW	1	171,212,383 (GRCm39)	missense	possibly damaging	0.46
R4886:Nectin4	UTSW	1	171,212,383 (GRCm39)	missense	possibly damaging	0.46
R5222:Nectin4	UTSW	1	171,212,825 (GRCm39)	splice site	probably null
R5264:Nectin4	UTSW	1	171,211,273 (GRCm39)	missense	probably benign	0.00
R5661:Nectin4	UTSW	1	171,212,738 (GRCm39)	missense	probably damaging	1.00
R6466:Nectin4	UTSW	1	171,214,321 (GRCm39)	missense	probably damaging	1.00
R6714:Nectin4	UTSW	1	171,198,218 (GRCm39)	start gained	probably benign
R7272:Nectin4	UTSW	1	171,214,212 (GRCm39)	missense	probably damaging	1.00
R7302:Nectin4	UTSW	1	171,214,203 (GRCm39)	nonsense	probably null
R7318:Nectin4	UTSW	1	171,208,031 (GRCm39)	missense	probably benign	0.16
R7669:Nectin4	UTSW	1	171,207,827 (GRCm39)	missense	probably benign	0.00
R7751:Nectin4	UTSW	1	171,211,326 (GRCm39)	critical splice donor site	probably null
R7912:Nectin4	UTSW	1	171,207,941 (GRCm39)	missense	possibly damaging	0.86
R7993:Nectin4	UTSW	1	171,211,322 (GRCm39)	missense	probably damaging	1.00
R8029:Nectin4	UTSW	1	171,214,255 (GRCm39)	missense	probably benign	0.04
R8306:Nectin4	UTSW	1	171,211,325 (GRCm39)	missense	probably null	1.00
R8314:Nectin4	UTSW	1	171,212,295 (GRCm39)	missense	probably benign	0.44
R8475:Nectin4	UTSW	1	171,212,280 (GRCm39)	nonsense	probably null
R8807:Nectin4	UTSW	1	171,211,282 (GRCm39)	missense	probably damaging	1.00
R9054:Nectin4	UTSW	1	171,214,351 (GRCm39)	missense	probably damaging	1.00
R9383:Nectin4	UTSW	1	171,213,251 (GRCm39)	missense	probably damaging	1.00
R9526:Nectin4	UTSW	1	171,210,209 (GRCm39)	nonsense	probably null
R9580:Nectin4	UTSW	1	171,211,324 (GRCm39)	missense	probably damaging	1.00
R9667:Nectin4	UTSW	1	171,210,165 (GRCm39)	missense	probably damaging	1.00
R9782:Nectin4	UTSW	1	171,214,192 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGTTTCCAAGCCCCTATGCC -3'
(R):5'- AAGAAGAGCCGAAGTTCCC -3'

Sequencing Primer
(F):5'- AGCCCCTATGCCTCTGGAAC -3'
(R):5'- AGAGCCGAAGTTCCCCCATG -3'

Posted On

2019-11-12