Mutagenetix > Incidental Mutation

Incidental Mutation 'R1439:Nectin1'

160852

Institutional Source

Beutler Lab

Gene Symbol

Nectin1

Ensembl Gene

ENSMUSG00000032012

Gene Name

nectin cell adhesion molecule 1

Synonyms

nectin-1, PRR1, HIgR, HveC, Cd111, PRR, Pvrl1

MMRRC Submission

039494-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.809) question?

Stock #

R1439 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

43655251-43718758 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 43703396 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 218 (E218G)

Ref Sequence

ENSEMBL: ENSMUSP00000034510 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000034510] [ENSMUST00000216893]

AlphaFold

Q9JKF6

PDB Structure

Solution structure of the third Immunoglobulin-like domain of nectin-1 [SOLUTION NMR]

Predicted Effect

possibly damaging
Transcript: ENSMUST00000034510
AA Change: E218G

PolyPhen 2 Score 0.780 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000034510
Gene: ENSMUSG00000032012
AA Change: E218G

Domain	Start	End	E-Value	Type
low complexity region	1	20	N/A	INTRINSIC
IG	36	143	8.51e-7	SMART
Pfam:C2-set_2	148	237	8.5e-21	PFAM
IG	254	334	1.28e-1	SMART
transmembrane domain	355	377	N/A	INTRINSIC
low complexity region	436	448	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000216893

Meta Mutation Damage Score

0.3736

Coding Region Coverage

1x: 98.8%
3x: 97.8%
10x: 94.4%
20x: 86.3%

Validation Efficiency

100% (72/72)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes an adhesion protein that plays a role in the organization of adherens junctions and tight junctions in epithelial and endothelial cells. The protein is a calcium(2+)-independent cell-cell adhesion molecule that belongs to the immunoglobulin superfamily and has 3 extracellular immunoglobulin-like loops, a single transmembrane domain (in some isoforms), and a cytoplasmic region. This protein acts as a receptor for glycoprotein D (gD) of herpes simplex viruses 1 and 2 (HSV-1, HSV-2), and pseudorabies virus (PRV) and mediates viral entry into epithelial and neuronal cells. Mutations in this gene cause cleft lip and palate/ectodermal dysplasia 1 syndrome (CLPED1) as well as non-syndromic cleft lip with or without cleft palate (CL/P). Alternative splicing results in multiple transcript variants encoding proteins with distinct C-termini. [provided by RefSeq, Oct 2009]
PHENOTYPE: Homozygous null mice exhibit eye abnormalities including microphthalmia, absent vitreous body, abnormal ciliary body, retinal layers, and lenses, and open eyelids at birth. [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
Agap1	A	G	1: 89,770,908 (GRCm39)	N499S	probably damaging	Het
AI661453	C	A	17: 47,777,587 (GRCm39)		probably benign	Het
Akap1	C	A	11: 88,735,577 (GRCm39)	G362*	probably null	Het
Alkbh1	A	G	12: 87,475,915 (GRCm39)	V289A	probably damaging	Het
Bnc2	C	T	4: 84,194,305 (GRCm39)	E1035K	probably benign	Het
C1s2	T	A	6: 124,607,126 (GRCm39)		probably benign	Het
Cabin1	A	G	10: 75,492,640 (GRCm39)	I1885T	probably damaging	Het
Col22a1	A	G	15: 71,824,226 (GRCm39)		probably benign	Het
Cpne4	A	T	9: 104,866,831 (GRCm39)	T248S	probably damaging	Het
Cracd	T	C	5: 76,988,757 (GRCm39)	V36A	probably damaging	Het
Cubn	T	C	2: 13,292,379 (GRCm39)	N3268S	probably damaging	Het
Ddx10	T	A	9: 53,151,787 (GRCm39)	K79N	probably damaging	Het
Dennd1a	A	C	2: 37,933,412 (GRCm39)	L131R	probably damaging	Het
Dnah9	T	C	11: 65,764,958 (GRCm39)	Y3862C	probably benign	Het
Eif3e	A	G	15: 43,141,824 (GRCm39)		probably benign	Het
Emsy	T	C	7: 98,250,048 (GRCm39)		probably benign	Het
Ep400	A	T	5: 110,833,344 (GRCm39)	D1959E	unknown	Het
Fpr-rs7	A	G	17: 20,333,869 (GRCm39)	I207T	probably benign	Het
Fubp3	C	A	2: 31,488,563 (GRCm39)	L140I	probably damaging	Het
Gas2l2	T	C	11: 83,318,298 (GRCm39)	D137G	probably damaging	Het
Git1	G	T	11: 77,397,244 (GRCm39)	R699L	possibly damaging	Het
Gnao1	T	A	8: 94,690,065 (GRCm39)	F27L	probably benign	Het
Hlx	G	T	1: 184,464,184 (GRCm39)	A52D	probably damaging	Het
Itga6	T	G	2: 71,664,378 (GRCm39)	Y505D	probably damaging	Het
Itgad	A	T	7: 127,782,178 (GRCm39)	T205S	probably benign	Het
Jakmip3	A	T	7: 138,631,375 (GRCm39)	Y574F	probably benign	Het
Laptm5	G	T	4: 130,653,520 (GRCm39)		probably benign	Het
Mlana	A	T	19: 29,684,252 (GRCm39)	R71S	probably benign	Het
Mroh2a	G	C	1: 88,185,524 (GRCm39)	E1510D	probably damaging	Het
Mus81	G	C	19: 5,535,145 (GRCm39)	R295G	probably benign	Het
Ncapd3	T	A	9: 26,998,862 (GRCm39)		probably null	Het
Nectin3	A	T	16: 46,268,757 (GRCm39)	Y548*	probably null	Het
Nif3l1	T	C	1: 58,487,102 (GRCm39)	F96S	probably damaging	Het
Ntrk1	A	G	3: 87,696,918 (GRCm39)		probably null	Het
Obsl1	C	A	1: 75,463,428 (GRCm39)	E1755*	probably null	Het
Or4p23	T	C	2: 88,577,178 (GRCm39)	E18G	possibly damaging	Het
Osbpl9	T	C	4: 108,958,353 (GRCm39)	D74G	probably damaging	Het
Osgin1	T	A	8: 120,169,852 (GRCm39)		probably null	Het
Otogl	A	G	10: 107,615,113 (GRCm39)	Y1931H	probably benign	Het
Pmepa1	A	G	2: 173,069,874 (GRCm39)	I227T	probably benign	Het
Pprc1	T	A	19: 46,052,175 (GRCm39)	N564K	possibly damaging	Het
Prkaa1	T	C	15: 5,194,225 (GRCm39)	F92S	probably damaging	Het
Ptprd	A	G	4: 75,984,437 (GRCm39)	F811L	probably damaging	Het
Rad54b	A	G	4: 11,606,152 (GRCm39)	K520R	possibly damaging	Het
Rbfox1	A	G	16: 7,148,297 (GRCm39)	T269A	possibly damaging	Het
Rfwd3	T	C	8: 112,004,920 (GRCm39)	Y554C	probably damaging	Het
Rfx2	A	T	17: 57,094,720 (GRCm39)	V208E	probably damaging	Het
Rgs22	G	T	15: 36,025,939 (GRCm39)		probably benign	Het
Rrbp1	A	G	2: 143,797,032 (GRCm39)		probably null	Het
Ryr2	C	T	13: 11,729,389 (GRCm39)		probably benign	Het
Sbno1	A	G	5: 124,522,523 (GRCm39)		probably benign	Het
Secisbp2	T	C	13: 51,833,759 (GRCm39)		probably benign	Het
Sgsm2	C	A	11: 74,759,964 (GRCm39)	R58L	probably benign	Het
Slc25a36	A	C	9: 96,975,126 (GRCm39)		probably benign	Het
Spink4	A	G	4: 40,929,121 (GRCm39)	T49A	possibly damaging	Het
Steap3	A	T	1: 120,155,550 (GRCm39)	F470I	probably damaging	Het
Stk10	A	G	11: 32,567,919 (GRCm39)	Q907R	probably damaging	Het
Tdrd5	A	G	1: 156,105,057 (GRCm39)	V446A	probably damaging	Het
Tmem117	G	A	15: 94,992,478 (GRCm39)	M379I	probably benign	Het
Trappc12	A	G	12: 28,797,160 (GRCm39)	L124P	possibly damaging	Het
Trim9	G	A	12: 70,297,867 (GRCm39)	H613Y	probably damaging	Het
Trio	A	G	15: 27,898,000 (GRCm39)	W371R	probably damaging	Het
Ulk4	G	C	9: 121,095,324 (GRCm39)	H110D	possibly damaging	Het
Upb1	T	C	10: 75,275,776 (GRCm39)	V387A	probably benign	Het
Utrn	A	T	10: 12,619,793 (GRCm39)	I284N	possibly damaging	Het
Vmn2r111	C	A	17: 22,790,097 (GRCm39)	W303L	probably benign	Het
Vmn2r15	G	T	5: 109,441,953 (GRCm39)	P160Q	probably damaging	Het
Wdtc1	A	G	4: 133,029,118 (GRCm39)	S323P	probably benign	Het
Zfp846	T	A	9: 20,505,393 (GRCm39)	C418S	possibly damaging	Het
Zfyve26	G	T	12: 79,298,937 (GRCm39)	P441Q	probably benign	Het

Other mutations in Nectin1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01618:Nectin1	APN	9	43,702,555 (GRCm39)	nonsense	probably null
IGL01939:Nectin1	APN	9	43,703,871 (GRCm39)	unclassified	probably benign
IGL01978:Nectin1	APN	9	43,703,444 (GRCm39)	missense	probably damaging	0.99
IGL02795:Nectin1	APN	9	43,714,849 (GRCm39)	missense	probably benign
K3955:Nectin1	UTSW	9	43,703,375 (GRCm39)	missense	probably damaging	1.00
R0563:Nectin1	UTSW	9	43,702,342 (GRCm39)	missense	probably benign
R1822:Nectin1	UTSW	9	43,702,374 (GRCm39)	nonsense	probably null
R4356:Nectin1	UTSW	9	43,703,802 (GRCm39)	missense	probably benign	0.22
R5153:Nectin1	UTSW	9	43,714,795 (GRCm39)	missense	probably damaging	0.99
R5516:Nectin1	UTSW	9	43,715,090 (GRCm39)	missense	probably benign	0.03
R5864:Nectin1	UTSW	9	43,702,607 (GRCm39)	missense	probably damaging	1.00
R6903:Nectin1	UTSW	9	43,703,179 (GRCm39)	missense	possibly damaging	0.95
R7791:Nectin1	UTSW	9	43,703,336 (GRCm39)	missense	probably benign	0.08
R7878:Nectin1	UTSW	9	43,715,198 (GRCm39)	missense	probably benign	0.10
R8046:Nectin1	UTSW	9	43,703,798 (GRCm39)	missense	probably benign	0.00
R8945:Nectin1	UTSW	9	43,703,237 (GRCm39)	missense	probably benign
R9459:Nectin1	UTSW	9	43,715,090 (GRCm39)	missense	probably benign
R9526:Nectin1	UTSW	9	43,702,369 (GRCm39)	missense	probably benign
R9744:Nectin1	UTSW	9	43,715,240 (GRCm39)	missense	probably damaging	0.97

Predicted Primers

PCR Primer
(F):5'- AGCAGATGCCCAGGCCATTTCAAC -3'
(R):5'- TCTATCACAGAACCTCAGCGGAAGC -3'

Sequencing Primer
(F):5'- AACTAATGCCATCGTGTTGC -3'
(R):5'- ACAGGGAGATTGCAGCATTTTG -3'

Posted On

2014-03-14