Mutagenetix > Incidental Mutation

Incidental Mutation 'R8029:Nectin4'

617796

Institutional Source

Beutler Lab

Gene Symbol

Nectin4

Ensembl Gene

ENSMUSG00000006411

Gene Name

nectin cell adhesion molecule 4

Synonyms

1200017F15Rik, Prr4, Pvrl4, nectin 4

MMRRC Submission

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.098) question?

Stock #

R8029 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

171370099-171388598 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 171386687 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 470 (D470G)

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: D470G

PolyPhen 2 Score 0.040 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000006578
Gene: ENSMUSG00000006411
AA Change: D470G

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: D445G

PolyPhen 2 Score 0.067 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000091883
Gene: ENSMUSG00000006411
AA Change: D445G

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: D470G

PolyPhen 2 Score 0.040 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000106917
Gene: ENSMUSG00000006411
AA Change: D470G

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: 99.7%
20x: 99.0%

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 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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700014D04Rik	T	C	13: 59,742,377	H543R	possibly damaging	Het
Acvr1c	A	G	2: 58,296,117	I118T	possibly damaging	Het
Alpk1	T	C	3: 127,729,285	D36G	possibly damaging	Het
Aox2	G	A	1: 58,343,668	V1036I	probably benign	Het
Arhgef1	T	C	7: 24,919,738	L468P	probably damaging	Het
Armc2	A	T	10: 41,927,000	L559Q	probably damaging	Het
Asb3	A	T	11: 31,101,180	R506*	probably null	Het
Asna1	T	C	8: 85,019,827	M131V	probably benign	Het
Aspm	A	G	1: 139,471,632	H1045R	probably benign	Het
Cacna1g	G	T	11: 94,409,738	R2099S	probably benign	Het
Cd177	C	T	7: 24,756,169	W309*	probably null	Het
Cd34	A	C	1: 194,958,552	M242L	probably benign	Het
Cdh24	T	A	14: 54,639,399	N49I	probably damaging	Het
Ces2b	A	G	8: 104,834,850	N192S	probably damaging	Het
Chsy3	A	G	18: 59,179,447	I331V	possibly damaging	Het
Disp1	A	G	1: 183,089,288	S523P	probably damaging	Het
Dlgap5	T	C	14: 47,416,440	H44R	probably benign	Het
Dnajc30	G	T	5: 135,064,332	A28S	probably benign	Het
Dsc2	C	T	18: 20,032,274	G881R	possibly damaging	Het
Exd1	A	T	2: 119,528,723	H226Q	probably damaging	Het
Gata6	T	A	18: 11,054,944	V291E	possibly damaging	Het
Gfi1b	A	T	2: 28,613,675		probably null	Het
Grk3	T	A	5: 112,961,642	I150L	probably benign	Het
Gstcd	C	T	3: 133,082,107	V277M	probably damaging	Het
Idua	T	C	5: 108,669,412	F17S	probably benign	Het
Ighg1	T	C	12: 113,329,145	K268R		Het
Lama1	G	T	17: 67,817,594	R2883M		Het
Lpar3	T	C	3: 146,240,963	M132T	probably benign	Het
Macf1	T	C	4: 123,444,892	T4351A	possibly damaging	Het
March6	A	G	15: 31,496,002		probably null	Het
Mbtps1	C	A	8: 119,547,805		probably benign	Het
Mctp1	T	C	13: 77,029,886	Y931H	probably damaging	Het
Mug2	A	G	6: 122,081,545		probably null	Het
Myh1	G	T	11: 67,211,240		probably null	Het
Mylk2	T	C	2: 152,920,299	S497P	probably damaging	Het
Nop2	C	T	6: 125,144,420	P722S	possibly damaging	Het
Nphp1	T	C	2: 127,741,116	T626A	probably benign	Het
Nudt9	C	T	5: 104,050,611		probably benign	Het
Olfr1145	A	G	2: 87,810,032	T71A	probably benign	Het
Olfr18	A	G	9: 20,314,347	F191S	possibly damaging	Het
Olfr512	T	A	7: 108,713,830	F159Y	possibly damaging	Het
Olfr835	T	C	9: 19,035,794	S224P	probably damaging	Het
Oplah	T	C	15: 76,305,696	Y143C	probably benign	Het
Osbpl1a	T	G	18: 12,914,521	E125D	probably benign	Het
P2ry1	C	A	3: 61,003,522	N27K	possibly damaging	Het
Palld	A	T	8: 61,877,312	I177N	probably damaging	Het
Plcl1	A	T	1: 55,696,078	I193L	probably benign	Het
Polr1a	T	A	6: 71,912,956	L53*	probably null	Het
Ppp1r9a	A	G	6: 5,057,518	E531G	possibly damaging	Het
Prex1	C	A	2: 166,575,603	Q1361H	probably benign	Het
Ptprc	T	C	1: 138,078,459	E795G	probably damaging	Het
Rars	C	T	11: 35,821,165	V295I	probably damaging	Het
Rnaseh2b	T	C	14: 62,353,548	V116A	possibly damaging	Het
Rnf43	T	A	11: 87,731,894	L480H	probably benign	Het
Rttn	A	G	18: 89,090,474	T1601A	not run	Het
Setd1a	C	G	7: 127,786,214	Q698E	probably benign	Het
Sh3gl3	T	C	7: 82,270,883	Y100H	probably benign	Het
Sis	T	C	3: 72,921,142	Y1200C	probably damaging	Het
Snx13	A	C	12: 35,119,886	H610P	probably damaging	Het
Spdl1	T	C	11: 34,822,592	R217G	probably benign	Het
Spop	G	A	11: 95,474,367	E113K	probably benign	Het
Sult2a3	G	A	7: 14,121,628	P101L	probably damaging	Het
Tbl1xr1	C	T	3: 22,200,436	H348Y	probably damaging	Het
Tmie	T	C	9: 110,867,487	T109A	possibly damaging	Het
Ttc12	A	G	9: 49,470,251	V140A	possibly damaging	Het
Ube2m	A	G	7: 13,036,597	L58P	probably damaging	Het
Urb1	A	G	16: 90,779,152	S839P	possibly damaging	Het
Vmn2r117	T	A	17: 23,477,770	D221V	probably benign	Het
Vps41	C	T	13: 18,823,785	Q263*	probably null	Het
Zfand3	A	T	17: 30,135,433	T75S	probably benign	Het
Zscan26	A	G	13: 21,445,350	C202R	probably damaging	Het

Other mutations in Nectin4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00819:Nectin4	APN	1	171384686	missense	probably damaging	1.00
IGL01558:Nectin4	APN	1	171384689	missense	probably benign	0.00
IGL02608:Nectin4	APN	1	171384773	missense	probably benign	0.05
R2047:Nectin4	UTSW	1	171385152	missense	possibly damaging	0.61
R2203:Nectin4	UTSW	1	171386229	missense	possibly damaging	0.78
R2518:Nectin4	UTSW	1	171380208	missense	probably benign	0.00
R4125:Nectin4	UTSW	1	171385733	missense	probably benign	0.02
R4708:Nectin4	UTSW	1	171385146	missense	probably benign	0.02
R4856:Nectin4	UTSW	1	171384815	missense	possibly damaging	0.46
R4886:Nectin4	UTSW	1	171384815	missense	possibly damaging	0.46
R5222:Nectin4	UTSW	1	171385257	splice site	probably null
R5264:Nectin4	UTSW	1	171383705	missense	probably benign	0.00
R5661:Nectin4	UTSW	1	171385170	missense	probably damaging	1.00
R6466:Nectin4	UTSW	1	171386753	missense	probably damaging	1.00
R6714:Nectin4	UTSW	1	171370650	start gained	probably benign
R7272:Nectin4	UTSW	1	171386644	missense	probably damaging	1.00
R7302:Nectin4	UTSW	1	171386635	nonsense	probably null
R7318:Nectin4	UTSW	1	171380463	missense	probably benign	0.16
R7669:Nectin4	UTSW	1	171380259	missense	probably benign	0.00
R7732:Nectin4	UTSW	1	171386678	missense	probably benign	0.00
R7751:Nectin4	UTSW	1	171383758	critical splice donor site	probably null
R7912:Nectin4	UTSW	1	171380373	missense	possibly damaging	0.86
R7993:Nectin4	UTSW	1	171383754	missense	probably damaging	1.00
R8306:Nectin4	UTSW	1	171383757	missense	probably null	1.00
R8314:Nectin4	UTSW	1	171384727	missense	probably benign	0.44
R8475:Nectin4	UTSW	1	171384712	nonsense	probably null
R8807:Nectin4	UTSW	1	171383714	missense	probably damaging	1.00
R9054:Nectin4	UTSW	1	171386783	missense	probably damaging	1.00
R9383:Nectin4	UTSW	1	171385683	missense	probably damaging	1.00
R9526:Nectin4	UTSW	1	171382641	nonsense	probably null
R9580:Nectin4	UTSW	1	171383756	missense	probably damaging	1.00
R9667:Nectin4	UTSW	1	171382597	missense	probably damaging	1.00
R9782:Nectin4	UTSW	1	171386624	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGGAACTACCATTACCCTTGC -3'
(R):5'- AAGAAGAGCCGAAGTTCCCC -3'

Sequencing Primer
(F):5'- GGAACTACCATTACCCTTGCTTCAC -3'
(R):5'- TCCCCCATGGAAGCAGAAG -3'

Posted On

2020-01-23