Mutagenetix > Incidental Mutation

Incidental Mutation 'R7232:Vcam1'

562534

Institutional Source

Beutler Lab

Gene Symbol

Vcam1

Ensembl Gene

ENSMUSG00000027962

Gene Name

vascular cell adhesion molecule 1

Synonyms

CD106, Vcam-1

MMRRC Submission

045303-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.554) question?

Stock #

R7232 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

115903669-115923337 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 115919628 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 213 (T213A)

Ref Sequence

ENSEMBL: ENSMUSP00000029574 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029574] [ENSMUST00000196309] [ENSMUST00000196449]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000029574
AA Change: T213A

PolyPhen 2 Score 0.707 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000029574
Gene: ENSMUSG00000027962
AA Change: T213A

Domain	Start	End	E-Value	Type
IG	32	113	2.41e-6	SMART
Pfam:C2-set	133	221	4.5e-27	PFAM
IGc2	237	298	2.09e-15	SMART
IGc2	326	390	8.38e-6	SMART
Pfam:C2-set	421	509	7.2e-26	PFAM
IGc2	525	586	7.35e-11	SMART
IG	608	686	2.25e-6	SMART
transmembrane domain	699	721	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000196309
AA Change: T219A

PolyPhen 2 Score 0.054 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000143260
Gene: ENSMUSG00000027962
AA Change: T219A

Domain	Start	End	E-Value	Type
signal peptide	1	30	N/A	INTRINSIC
IG	38	119	1e-8	SMART
Pfam:C2-set	139	227	1.4e-25	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000196449
AA Change: T213A

PolyPhen 2 Score 0.024 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000142876
Gene: ENSMUSG00000027962
AA Change: T213A

Domain	Start	End	E-Value	Type
IG	32	113	2.41e-6	SMART
Pfam:C2-set	133	221	1.3e-27	PFAM
IGc2	237	298	2.09e-15	SMART
transmembrane domain	322	344	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

99% (80/81)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the Ig superfamily and encodes a cell surface sialoglycoprotein expressed by cytokine-activated endothelium. This type I membrane protein mediates leukocyte-endothelial cell adhesion and signal transduction, and may play a role in the development of artherosclerosis and rheumatoid arthritis. Three alternatively spliced transcripts encoding different isoforms have been described for this gene. [provided by RefSeq, Dec 2010]
PHENOTYPE: Most homozygous null mutants die by embryonic day 12.5 due to defective placenta and failure of chorion/allantois fusion, and heart developmental anomalies. Survivors are generally normal, but have high numbers of circulating blood mononuclear leukocytes. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930433I11Rik	G	A	7: 40,642,603 (GRCm39)	G91S	probably damaging	Het
Adam21	T	G	12: 81,607,330 (GRCm39)	N144T	probably damaging	Het
Adgrg7	T	C	16: 56,597,515 (GRCm39)		probably null	Het
Angpt4	T	C	2: 151,771,460 (GRCm39)	S259P	possibly damaging	Het
Aqr	A	C	2: 113,936,363 (GRCm39)	L1320R	probably damaging	Het
Arhgef10	G	A	8: 14,990,323 (GRCm39)	G266D	probably benign	Het
Bop1	A	G	15: 76,337,546 (GRCm39)	V693A	probably damaging	Het
Cd86	CA	CAA	16: 36,426,917 (GRCm39)		probably null	Het
Cdc5l	A	G	17: 45,738,863 (GRCm39)		probably null	Het
Cfap46	C	A	7: 139,197,493 (GRCm39)	R2126L	unknown	Het
Chek2	T	C	5: 111,008,781 (GRCm39)	V304A	probably damaging	Het
Cntnap4	T	A	8: 113,391,731 (GRCm39)		probably null	Het
Ctps1	C	A	4: 120,405,321 (GRCm39)	G374C	probably damaging	Het
Defa27	A	T	8: 21,805,625 (GRCm39)	I22F	probably damaging	Het
Dnah14	T	C	1: 181,584,928 (GRCm39)	S3220P	probably damaging	Het
Dop1b	T	G	16: 93,557,373 (GRCm39)		probably null	Het
Dpysl5	G	A	5: 30,949,642 (GRCm39)	V471I	probably benign	Het
Duoxa1	T	A	2: 122,135,728 (GRCm39)	I124F	probably damaging	Het
Eif4enif1	A	G	11: 3,165,678 (GRCm39)	E85G	possibly damaging	Het
Eogt	T	A	6: 97,096,944 (GRCm39)	I355F	probably damaging	Het
Epha7	T	A	4: 28,951,279 (GRCm39)	V800E	probably damaging	Het
Evi5l	A	G	8: 4,255,906 (GRCm39)	Q633R	possibly damaging	Het
Fam170a	T	C	18: 50,414,728 (GRCm39)	Y125H	probably damaging	Het
Fbxo15	T	C	18: 84,980,747 (GRCm39)	Y241H	probably damaging	Het
Gbe1	T	C	16: 70,233,828 (GRCm39)	I235T	possibly damaging	Het
Gfra3	C	T	18: 34,844,234 (GRCm39)	R102Q	probably damaging	Het
Gjd4	C	T	18: 9,280,380 (GRCm39)	G233S	probably damaging	Het
Gm29106	C	T	1: 118,127,291 (GRCm39)	P328S	probably damaging	Het
Hgfac	G	T	5: 35,204,258 (GRCm39)	R507L	probably damaging	Het
Jakmip3	A	G	7: 138,609,355 (GRCm39)	K153R	probably benign	Het
Kcnc1	T	A	7: 46,077,383 (GRCm39)	V395E	probably damaging	Het
Krt6b	T	C	15: 101,586,577 (GRCm39)	D304G	probably damaging	Het
Ldha	T	C	7: 46,500,323 (GRCm39)	Y174H	probably benign	Het
Lgi4	G	A	7: 30,766,776 (GRCm39)	V268M	possibly damaging	Het
Lpar3	T	G	3: 145,947,061 (GRCm39)		probably null	Het
Lrp3	T	C	7: 34,905,477 (GRCm39)	D103G	probably damaging	Het
Marchf5	G	A	19: 37,194,713 (GRCm39)		probably null	Het
Muc5b	A	T	7: 141,419,866 (GRCm39)	H4115L	possibly damaging	Het
Myh13	G	A	11: 67,239,672 (GRCm39)	D741N	probably damaging	Het
Naglu	A	T	11: 100,967,252 (GRCm39)	I401F	probably damaging	Het
Ncam2	T	A	16: 81,309,759 (GRCm39)	N416K	probably damaging	Het
Ncan	A	G	8: 70,564,738 (GRCm39)	L292S	probably damaging	Het
Nkiras1	T	C	14: 18,276,732 (GRCm38)	V7A	probably damaging	Het
Nlrp4c	T	A	7: 6,068,708 (GRCm39)	L203*	probably null	Het
Nscme3l	A	T	19: 5,553,659 (GRCm39)	S41T	possibly damaging	Het
Onecut2	T	A	18: 64,474,633 (GRCm39)	W395R	probably damaging	Het
Or10a2	T	A	7: 106,673,062 (GRCm39)	I9K	probably benign	Het
Pak6	T	A	2: 118,524,003 (GRCm39)	V386E	probably damaging	Het
Pias2	A	G	18: 77,220,931 (GRCm39)	S396G	probably benign	Het
Plxna2	T	A	1: 194,394,568 (GRCm39)	L483H	probably damaging	Het
Prss36	G	T	7: 127,534,763 (GRCm39)	R484S	probably benign	Het
Ptpn21	A	T	12: 98,654,996 (GRCm39)	V657E	probably benign	Het
Rassf2	T	C	2: 131,838,332 (GRCm39)	E318G	probably damaging	Het
Rp1	A	C	1: 4,298,824 (GRCm39)	S623A	unknown	Het
Runx2	G	A	17: 45,125,079 (GRCm39)	P80L	probably damaging	Het
Scn11a	T	A	9: 119,588,982 (GRCm39)	E1308V	probably damaging	Het
Serpina3c	A	T	12: 104,115,771 (GRCm39)	S258T	possibly damaging	Het
Slit3	A	G	11: 35,501,516 (GRCm39)	T417A	possibly damaging	Het
Sostdc1	C	A	12: 36,367,310 (GRCm39)	A162E	possibly damaging	Het
Sox13	A	T	1: 133,312,129 (GRCm39)		probably null	Het
Sox8	G	T	17: 25,786,514 (GRCm39)	S396R	probably benign	Het
Sult2a3	A	T	7: 13,816,685 (GRCm39)	F164L	possibly damaging	Het
Susd2	T	C	10: 75,475,685 (GRCm39)	Y438C	probably damaging	Het
Tas2r106	T	G	6: 131,655,810 (GRCm39)	T14P	probably damaging	Het
Tcf25	T	A	8: 124,127,800 (GRCm39)		probably null	Het
Tenm3	G	A	8: 48,688,970 (GRCm39)	R2206W	probably damaging	Het
Tep1	A	G	14: 51,081,789 (GRCm39)	L471P	unknown	Het
Ticrr	A	T	7: 79,343,490 (GRCm39)	K1118N	probably damaging	Het
Tlr5	G	A	1: 182,801,064 (GRCm39)	E123K	probably benign	Het
Ttn	ATATCTCTCCAGAGCCTCCCCTGGAGGAGTGGAGTATCTCTCCAGAGCCTCCCCTGGAGGAGTGGAGTATCTCTCCAGAGCCTCCCCTG	ATATCTCTCCAGAGCCTCCCCTGGAGGAGTGGAGTATCTCTCCAGAGCCTCCCCTG	2: 76,746,150 (GRCm39)		probably benign	Het
U2surp	A	G	9: 95,375,770 (GRCm39)	V141A	probably benign	Het
Unc79	T	A	12: 103,100,734 (GRCm39)	S2050T	possibly damaging	Het
Usp13	A	G	3: 32,920,020 (GRCm39)	D235G	probably benign	Het
Vmn2r60	T	A	7: 41,786,166 (GRCm39)	I323N	possibly damaging	Het
Vps13b	A	G	15: 35,877,703 (GRCm39)	I2892M	probably damaging	Het
Wnt5a	T	A	14: 28,240,329 (GRCm39)	S160T	probably benign	Het
Zar1	G	A	5: 72,738,294 (GRCm39)	P36L	possibly damaging	Het
Zfp773	A	T	7: 7,135,984 (GRCm39)	M204K	probably benign	Het
Zhx1	T	C	15: 57,916,465 (GRCm39)	T594A	probably benign	Het

Other mutations in Vcam1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00717:Vcam1	APN	3	115,908,120 (GRCm39)	missense	possibly damaging	0.85
IGL01546:Vcam1	APN	3	115,909,591 (GRCm39)	missense	possibly damaging	0.86
IGL01548:Vcam1	APN	3	115,909,600 (GRCm39)	missense	probably benign	0.06
IGL02070:Vcam1	APN	3	115,919,646 (GRCm39)	missense	probably benign	0.07
IGL02353:Vcam1	APN	3	115,909,543 (GRCm39)	missense	possibly damaging	0.53
IGL02360:Vcam1	APN	3	115,909,543 (GRCm39)	missense	possibly damaging	0.53
K7371:Vcam1	UTSW	3	115,918,298 (GRCm39)	missense	probably benign	0.00
R0310:Vcam1	UTSW	3	115,908,065 (GRCm39)	missense	possibly damaging	0.93
R0319:Vcam1	UTSW	3	115,909,709 (GRCm39)	missense	probably benign	0.01
R0468:Vcam1	UTSW	3	115,909,595 (GRCm39)	nonsense	probably null
R0638:Vcam1	UTSW	3	115,910,908 (GRCm39)	missense	possibly damaging	0.71
R1070:Vcam1	UTSW	3	115,904,552 (GRCm39)	missense	possibly damaging	0.96
R1728:Vcam1	UTSW	3	115,908,164 (GRCm39)	missense	probably benign	0.16
R1784:Vcam1	UTSW	3	115,908,164 (GRCm39)	missense	probably benign	0.16
R1956:Vcam1	UTSW	3	115,919,606 (GRCm39)	missense	probably damaging	1.00
R1957:Vcam1	UTSW	3	115,919,606 (GRCm39)	missense	probably damaging	1.00
R3052:Vcam1	UTSW	3	115,918,079 (GRCm39)	splice site	probably null
R3832:Vcam1	UTSW	3	115,908,140 (GRCm39)	missense	possibly damaging	0.71
R4297:Vcam1	UTSW	3	115,910,892 (GRCm39)	missense	probably benign
R4801:Vcam1	UTSW	3	115,909,584 (GRCm39)	missense	probably damaging	0.98
R4802:Vcam1	UTSW	3	115,909,584 (GRCm39)	missense	probably damaging	0.98
R4970:Vcam1	UTSW	3	115,910,941 (GRCm39)	missense	probably benign	0.00
R5073:Vcam1	UTSW	3	115,918,037 (GRCm39)	missense	probably damaging	1.00
R5074:Vcam1	UTSW	3	115,918,037 (GRCm39)	missense	probably damaging	1.00
R5112:Vcam1	UTSW	3	115,910,941 (GRCm39)	missense	probably benign	0.00
R5597:Vcam1	UTSW	3	115,919,651 (GRCm39)	missense	probably damaging	0.99
R6035:Vcam1	UTSW	3	115,919,606 (GRCm39)	missense	probably damaging	1.00
R6035:Vcam1	UTSW	3	115,919,606 (GRCm39)	missense	probably damaging	1.00
R6120:Vcam1	UTSW	3	115,918,049 (GRCm39)	missense	probably damaging	0.99
R6617:Vcam1	UTSW	3	115,919,711 (GRCm39)	missense	possibly damaging	0.48
R7350:Vcam1	UTSW	3	115,908,211 (GRCm39)	missense	probably damaging	0.99
R7384:Vcam1	UTSW	3	115,910,877 (GRCm39)	missense	possibly damaging	0.81
R7571:Vcam1	UTSW	3	115,908,032 (GRCm39)	nonsense	probably null
R7606:Vcam1	UTSW	3	115,914,704 (GRCm39)	missense	possibly damaging	0.91
R7742:Vcam1	UTSW	3	115,909,734 (GRCm39)	missense	possibly damaging	0.71
R8151:Vcam1	UTSW	3	115,918,128 (GRCm39)	missense	possibly damaging	0.71
R8965:Vcam1	UTSW	3	115,922,422 (GRCm39)	nonsense	probably null
R8997:Vcam1	UTSW	3	115,910,977 (GRCm39)	missense	probably benign
R9182:Vcam1	UTSW	3	115,911,004 (GRCm39)	missense	probably benign
R9224:Vcam1	UTSW	3	115,904,592 (GRCm39)	nonsense	probably null
R9540:Vcam1	UTSW	3	115,911,019 (GRCm39)	missense	possibly damaging	0.78
R9725:Vcam1	UTSW	3	115,922,287 (GRCm39)	missense	possibly damaging	0.51
R9729:Vcam1	UTSW	3	115,911,105 (GRCm39)	missense	probably damaging	1.00
Z1176:Vcam1	UTSW	3	115,922,990 (GRCm39)	missense	not run

Predicted Primers

PCR Primer
(F):5'- TCTCAGCTAACAAGGGGAGATG -3'
(R):5'- CCAGCTCATGAACAGACAGGAG -3'

Sequencing Primer
(F):5'- GTGCTCTAAACCTAAAATCCGGTGTC -3'
(R):5'- CAGCTCATGAACAGACAGGAGTTTTC -3'

Posted On

2019-06-26