Mutagenetix > Incidental Mutation

Incidental Mutation 'R0563:Nectin1'

46015

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

038754-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.809) question?

Stock #

R0563 (G1)

Quality Score

184

Status

Validated

Chromosome

Chromosomal Location

43655251-43718758 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 43702342 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 30 (T30A)

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

probably benign
Transcript: ENSMUST00000034510
AA Change: T30A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000034510
Gene: ENSMUSG00000032012
AA Change: T30A

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

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.6%
20x: 93.3%

Validation Efficiency

98% (52/53)

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: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrb3	G	T	1: 25,586,635 (GRCm39)	P146T	probably damaging	Het
Ambn	A	C	5: 88,611,309 (GRCm39)	N163T	probably benign	Het
Ankrd36	A	T	11: 5,579,322 (GRCm39)	E870D	probably benign	Het
Cdc123	T	C	2: 5,803,212 (GRCm39)	N269S	probably benign	Het
Cdc7	A	T	5: 107,120,776 (GRCm39)		probably benign	Het
Cdh2	A	T	18: 16,762,738 (GRCm39)	V402D	possibly damaging	Het
Cwc27	C	A	13: 104,797,865 (GRCm39)	E365*	probably null	Het
Dcdc5	G	A	2: 106,180,035 (GRCm39)		noncoding transcript	Het
Eif4g3	T	C	4: 137,903,151 (GRCm39)		probably benign	Het
Elovl4	C	T	9: 83,667,087 (GRCm39)		probably null	Het
Fhl5	T	G	4: 25,213,610 (GRCm39)	I109L	probably damaging	Het
Gm16181	A	G	17: 35,442,872 (GRCm39)		probably benign	Het
Gna14	A	G	19: 16,585,483 (GRCm39)	Y287C	probably benign	Het
Greb1	A	T	12: 16,730,268 (GRCm39)	C1720S	probably benign	Het
Gypa	T	A	8: 81,236,089 (GRCm39)	S165T	probably benign	Het
Hephl1	T	C	9: 14,993,241 (GRCm39)	D531G	probably damaging	Het
Hsf2bp	A	T	17: 32,226,692 (GRCm39)	L221Q	probably damaging	Het
Itsn1	A	G	16: 91,617,684 (GRCm39)		probably benign	Het
Kif7	T	C	7: 79,352,020 (GRCm39)	E914G	probably benign	Het
Lrp1b	T	C	2: 40,640,926 (GRCm39)	D3506G	probably benign	Het
Lrrc28	T	C	7: 67,195,135 (GRCm39)	N225S	probably damaging	Het
Lysmd4	T	A	7: 66,875,925 (GRCm39)	L196Q	probably benign	Het
Megf8	T	C	7: 25,041,820 (GRCm39)	C1245R	probably damaging	Het
Mgat4f	A	G	1: 134,317,777 (GRCm39)	K183R	probably benign	Het
Mib2	C	T	4: 155,743,917 (GRCm39)	G42S	probably damaging	Het
Mindy2	T	A	9: 70,538,334 (GRCm39)	I334L	possibly damaging	Het
Mrm1	A	G	11: 84,705,539 (GRCm39)	S287P	probably damaging	Het
Ncor1	A	G	11: 62,234,056 (GRCm39)	I382T	probably damaging	Het
Nelfe	A	G	17: 35,073,215 (GRCm39)	E250G	possibly damaging	Het
Nsd1	C	A	13: 55,394,391 (GRCm39)	T767K	possibly damaging	Het
Or1i2	G	A	10: 78,448,467 (GRCm39)	P3S	probably benign	Het
Or1j18	A	T	2: 36,625,013 (GRCm39)	K227*	probably null	Het
Or4e5	T	A	14: 52,727,714 (GRCm39)	K236*	probably null	Het
Or5b111	A	G	19: 13,291,112 (GRCm39)	I179T	probably benign	Het
Pcnx1	A	G	12: 81,964,718 (GRCm39)	D295G	probably damaging	Het
Pex14	A	G	4: 149,046,003 (GRCm39)	V309A	possibly damaging	Het
Phf14	C	T	6: 11,933,600 (GRCm39)		probably benign	Het
Pnpla6	A	G	8: 3,573,333 (GRCm39)	D399G	possibly damaging	Het
Prim1	A	G	10: 127,862,423 (GRCm39)	D340G	probably damaging	Het
Rb1	A	G	14: 73,454,207 (GRCm39)	F564L	probably damaging	Het
Rcc1l	G	C	5: 134,205,394 (GRCm39)	R54G	probably benign	Het
Rnf151	G	A	17: 24,936,430 (GRCm39)		probably benign	Het
Rnf40	T	C	7: 127,192,048 (GRCm39)	L398P	probably damaging	Het
Robo1	C	T	16: 72,769,174 (GRCm39)	T531I	probably benign	Het
Rps6ka2	A	T	17: 7,521,836 (GRCm39)	I198F	probably damaging	Het
Sgk2	T	C	2: 162,846,164 (GRCm39)	L264P	probably damaging	Het
Slc26a6	T	A	9: 108,734,869 (GRCm39)	I281N	probably damaging	Het
Tnxb	A	T	17: 34,935,921 (GRCm39)	K2657N	probably benign	Het
Tor1aip1	G	A	1: 155,911,554 (GRCm39)	T143M	probably damaging	Het
Tpr	A	G	1: 150,284,609 (GRCm39)	D358G	probably benign	Het
Vstm2b	T	C	7: 40,551,899 (GRCm39)	S76P	probably damaging	Het
Wdr33	A	G	18: 32,019,792 (GRCm39)	K488R	possibly damaging	Het
Ythdc2	T	A	18: 44,997,915 (GRCm39)		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
R1439:Nectin1	UTSW	9	43,703,396 (GRCm39)	missense	possibly damaging	0.78
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'- GCTGCGTAACACATACACATGCAAA -3'
(R):5'- ACACACCCATAGTCGGGTTGTAGAT -3'

Sequencing Primer
(F):5'- ttgtgggtgtgtggggg -3'
(R):5'- AAGCTACAGTGCAGTACCAC -3'

Posted On

2013-06-11