Mutagenetix > Incidental Mutation

Incidental Mutation 'R8314:Nectin4'

641543

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

067719-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.105) question?

Stock #

R8314 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

171197741-171215855 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 171212295 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 298 (T298A)

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: T298A

PolyPhen 2 Score 0.437 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000006578
Gene: ENSMUSG00000006411
AA Change: T298A

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: T298A

PolyPhen 2 Score 0.383 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000091883
Gene: ENSMUSG00000006411
AA Change: T298A

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: T298A

PolyPhen 2 Score 0.437 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000106917
Gene: ENSMUSG00000006411
AA Change: T298A

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

Coding Region Coverage

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

Validation Efficiency

100% (67/67)

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: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110059G10Rik	T	A	9: 122,777,993 (GRCm39)	T84S	probably benign	Het
4930533K18Rik	A	G	10: 70,711,106 (GRCm39)	T76A	noncoding transcript	Het
Adgrl1	C	T	8: 84,665,018 (GRCm39)	T1235I	probably damaging	Het
Ak4	C	T	4: 101,320,782 (GRCm39)	T197M	possibly damaging	Het
Alkal2	G	T	12: 30,934,850 (GRCm39)	G23V	probably damaging	Het
Alox12e	T	C	11: 70,206,998 (GRCm39)	M603V	possibly damaging	Het
Ap3d1	A	T	10: 80,559,373 (GRCm39)	I267N	possibly damaging	Het
Arhgef2	T	A	3: 88,528,600 (GRCm39)	I12N	probably benign	Het
Asnsd1	A	T	1: 53,385,814 (GRCm39)	M520K	probably damaging	Het
B3galt5	T	C	16: 96,116,649 (GRCm39)	L94P	probably damaging	Het
Birc2	T	C	9: 7,872,942 (GRCm39)		probably benign	Het
Cd177	T	C	7: 24,450,013 (GRCm39)	S541G	probably benign	Het
Cdh8	T	C	8: 99,898,011 (GRCm39)	D434G	probably damaging	Het
Cdkn3	A	T	14: 47,007,330 (GRCm39)		silent	Het
Ciita	A	T	16: 10,328,852 (GRCm39)	R379W	probably damaging	Het
Cntrl	T	A	2: 35,065,155 (GRCm39)	M2153K	probably benign	Het
Csmd1	A	T	8: 16,208,258 (GRCm39)	D1232E	probably benign	Het
Cyp4a30b	A	C	4: 115,315,535 (GRCm39)	H252P	probably benign	Het
Dad1	G	A	14: 54,491,269 (GRCm39)	R11W	probably damaging	Het
Ddit3	A	G	10: 127,131,590 (GRCm39)		probably null	Het
Dusp22	G	A	13: 30,892,914 (GRCm39)		probably benign	Het
Dzank1	A	G	2: 144,344,878 (GRCm39)	L293P	probably damaging	Het
Edf1	A	G	2: 25,447,977 (GRCm39)	D5G	probably damaging	Het
Entrep3	T	C	3: 89,095,453 (GRCm39)		probably null	Het
Ep400	T	A	5: 110,903,619 (GRCm39)	M327L	unknown	Het
Fam135a	A	T	1: 24,061,002 (GRCm39)	H1341Q	possibly damaging	Het
Fbxl3	C	T	14: 103,326,876 (GRCm39)	V169I	probably benign	Het
Gm4787	A	G	12: 81,425,909 (GRCm39)	L83P	probably damaging	Het
Habp4	A	G	13: 64,332,565 (GRCm39)	E392G	probably damaging	Het
Hspg2	C	A	4: 137,266,986 (GRCm39)	P1997Q	probably benign	Het
Ints9	T	C	14: 65,266,479 (GRCm39)	S444P	probably damaging	Het
Kif18b	G	A	11: 102,803,900 (GRCm39)	S420L	probably benign	Het
Klhl17	T	A	4: 156,318,470 (GRCm39)	M51L	probably benign	Het
Kmt2b	C	T	7: 30,278,347 (GRCm39)	E1555K	probably damaging	Het
Malrd1	T	A	2: 15,757,643 (GRCm39)	D972E	unknown	Het
Mapk8ip3	A	T	17: 25,120,748 (GRCm39)	S805R	probably benign	Het
Mmp13	G	A	9: 7,272,931 (GRCm39)	C97Y	probably damaging	Het
Moxd1	T	A	10: 24,128,438 (GRCm39)	N163K	possibly damaging	Het
Nbea	T	C	3: 55,916,672 (GRCm39)	I863V	probably damaging	Het
Net1	T	C	13: 3,962,672 (GRCm39)		probably benign	Het
Ntn1	T	C	11: 68,276,450 (GRCm39)	D166G	probably damaging	Het
Opa3	C	A	7: 18,978,940 (GRCm39)	A135E	possibly damaging	Het
Or1e31	T	G	11: 73,690,568 (GRCm39)	N5T	noncoding transcript	Het
Or4c3d	T	C	2: 89,882,441 (GRCm39)	T76A	probably benign	Het
Or51v14	T	C	7: 103,261,254 (GRCm39)	Q102R	probably damaging	Het
Or5w14	A	G	2: 87,541,546 (GRCm39)	F235L	probably benign	Het
Or8g30	A	G	9: 39,230,601 (GRCm39)	F103S	probably damaging	Het
Osbpl5	T	C	7: 143,248,833 (GRCm39)	I608V	probably benign	Het
Phc1	A	C	6: 122,297,937 (GRCm39)	S782R	unknown	Het
Phf8-ps	C	A	17: 33,286,038 (GRCm39)	A255S	probably benign	Het
Pip5k1b	T	A	19: 24,332,563 (GRCm39)	T374S	probably benign	Het
Prkaa1	A	G	15: 5,208,354 (GRCm39)	S541G	probably damaging	Het
Ptpn20	A	G	14: 33,344,504 (GRCm39)	N143D	possibly damaging	Het
Rabep1	A	G	11: 70,784,486 (GRCm39)	D207G	possibly damaging	Het
Rbbp8	G	A	18: 11,853,682 (GRCm39)	M296I	probably benign	Het
Recql4	C	A	15: 76,594,380 (GRCm39)	R46L	probably damaging	Het
Scgb2b18	T	C	7: 32,872,582 (GRCm39)	I74M	probably benign	Het
Shc4	A	G	2: 125,497,536 (GRCm39)	I391T	possibly damaging	Het
Slc38a4	A	G	15: 96,908,190 (GRCm39)	F184L	probably benign	Het
Slc7a6	A	G	8: 106,895,590 (GRCm39)		probably benign	Het
Smim13	G	T	13: 41,426,110 (GRCm39)	G49*	probably null	Het
Tbc1d19	A	G	5: 54,054,389 (GRCm39)	D459G	probably damaging	Het
Tnpo1	T	C	13: 99,021,133 (GRCm39)	N82S	possibly damaging	Het
Tpp2	G	A	1: 43,973,387 (GRCm39)	V47I	probably benign	Het
Umodl1	G	T	17: 31,203,806 (GRCm39)	A540S	probably damaging	Het
Vmn2r83	G	A	10: 79,317,313 (GRCm39)	V519I	possibly damaging	Het
Zfp641	T	C	15: 98,188,464 (GRCm39)	I139V	probably damaging	Het
Zfyve21	A	T	12: 111,789,715 (GRCm39)	I60F	probably benign	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
R7732:Nectin4	UTSW	1	171,214,246 (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
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'- GAATCATGTGGGATGGCATGC -3'
(R):5'- TGGGACAGACACATCCACAG -3'

Sequencing Primer
(F):5'- GGATCTTCCCCCAAGTGTGTG -3'
(R):5'- CAGCTTAATCCTTTCCAAAACATATC -3'

Posted On

2020-07-28