Mutagenetix > Incidental Mutation

Incidental Mutation 'R4923:Clstn1'

378766

Institutional Source

Beutler Lab

Gene Symbol

Clstn1

Ensembl Gene

ENSMUSG00000039953

Gene Name

calsyntenin 1

Synonyms

Cst-1, alcadein alpha, calsyntenin-1, 1810034E21Rik

MMRRC Submission

042525-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4923 (G1)

Quality Score

143

Status

Validated

Chromosome

Chromosomal Location

149670925-149733356 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 149729486 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 747 (V747A)

Ref Sequence

ENSEMBL: ENSMUSP00000101316 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038859] [ENSMUST00000039144] [ENSMUST00000105688] [ENSMUST00000105690] [ENSMUST00000105691] [ENSMUST00000118704] [ENSMUST00000122059] [ENSMUST00000177654]

AlphaFold

Q9EPL2

Predicted Effect

probably benign
Transcript: ENSMUST00000038859

SMART Domains

Protein: ENSMUSP00000036434
Gene: ENSMUSG00000039936

Domain	Start	End	E-Value	Type
PI3K_p85B	31	108	2.24e-26	SMART
PI3K_rbd	174	281	1.3e-13	SMART
PI3K_C2	309	412	1.87e-28	SMART
PI3Ka	496	685	8.56e-87	SMART
PI3Kc	776	1042	5.65e-128	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000039144
AA Change: V757A

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

SMART Domains

Protein: ENSMUSP00000036962
Gene: ENSMUSG00000039953
AA Change: V757A

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
CA	59	162	1.25e-11	SMART
CA	185	263	1.03e-3	SMART
Pfam:Laminin_G_3	365	510	3.3e-9	PFAM
low complexity region	663	674	N/A	INTRINSIC
transmembrane domain	860	882	N/A	INTRINSIC
coiled coil region	915	949	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000105688

SMART Domains

Protein: ENSMUSP00000101313
Gene: ENSMUSG00000039936

Domain	Start	End	E-Value	Type
PI3K_p85B	31	108	2.24e-26	SMART
PI3K_rbd	174	281	1.3e-13	SMART
PI3K_C2	309	412	1.87e-28	SMART
PI3Ka	496	685	8.56e-87	SMART
PI3Kc	775	1041	5.65e-128	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000105690

SMART Domains

Protein: ENSMUSP00000101315
Gene: ENSMUSG00000039936

Domain	Start	End	E-Value	Type
PI3K_p85B	31	108	2.24e-26	SMART
PI3K_rbd	174	281	1.3e-13	SMART
PI3K_C2	309	412	1.87e-28	SMART
PI3Ka	496	688	1.22e-82	SMART
PI3Kc	778	1044	5.65e-128	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000105691
AA Change: V747A

PolyPhen 2 Score 0.068 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000101316
Gene: ENSMUSG00000039953
AA Change: V747A

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
CA	59	152	2.91e-12	SMART
CA	175	253	1.03e-3	SMART
Pfam:Laminin_G_3	350	544	1.1e-12	PFAM
low complexity region	653	664	N/A	INTRINSIC
transmembrane domain	850	872	N/A	INTRINSIC
coiled coil region	905	939	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000118704

SMART Domains

Protein: ENSMUSP00000112863
Gene: ENSMUSG00000039936

Domain	Start	End	E-Value	Type
PI3K_p85B	31	108	2.24e-26	SMART
PI3K_rbd	174	281	1.3e-13	SMART
PI3K_C2	309	412	1.87e-28	SMART
PI3Ka	496	687	1.8e-80	SMART
PI3Kc	777	1043	5.65e-128	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000122059

SMART Domains

Protein: ENSMUSP00000113844
Gene: ENSMUSG00000039936

Domain	Start	End	E-Value	Type
PI3K_p85B	31	108	2.24e-26	SMART
PI3K_rbd	174	281	1.3e-13	SMART
PI3K_C2	309	408	6.47e-23	SMART
PI3Ka	492	681	8.56e-87	SMART
PI3Kc	771	1037	5.65e-128	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000177654

SMART Domains

Protein: ENSMUSP00000136045
Gene: ENSMUSG00000039936

Domain	Start	End	E-Value	Type
PI3K_p85B	31	108	2.24e-26	SMART
PI3K_rbd	174	281	1.3e-13	SMART
PI3K_C2	309	412	1.87e-28	SMART
PI3Ka	496	688	1.22e-82	SMART
PI3Kc	778	1044	5.65e-128	SMART

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 96.0%
20x: 91.3%

Validation Efficiency

98% (107/109)

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 calsyntenin family, a subset of the cadherin superfamily. The encoded transmembrane protein, also known as alcadein-alpha, is thought to bind to kinesin-1 motors to mediate the axonal anterograde transport of certain types of vesicle. Amyloid precursor protein (APP) is trafficked via these vesicles and so this protein is being investigated to see how it might contribute to the mechanisms underlying Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]
PHENOTYPE: Juvenile mice homozygous for a null allele show reduced basal excitatory synaptic transmission, abnormal excitatory postsynaptic currents, enhanced NMDA receptor-dependent long term potentiation, and delayed dendritic spine maturation in CA1 hippocampal pyramidal cells. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 95 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aim2	A	G	1: 173,287,372 (GRCm39)	D124G	probably benign	Het
Akr1c6	T	C	13: 4,504,494 (GRCm39)	M293T	probably damaging	Het
Albfm1	A	G	5: 90,709,158 (GRCm39)	T23A	probably benign	Het
Ankhd1	A	G	18: 36,722,505 (GRCm39)	T343A	probably damaging	Het
Ano2	T	C	6: 125,880,018 (GRCm39)		probably benign	Het
Arfgap2	G	A	2: 91,104,004 (GRCm39)	G353R	probably damaging	Het
Armc3	A	G	2: 19,297,791 (GRCm39)		probably null	Het
Atp11b	T	C	3: 35,889,528 (GRCm39)		probably null	Het
Brd4	A	G	17: 32,418,214 (GRCm39)	M13T	probably benign	Het
Btd	T	A	14: 31,384,044 (GRCm39)	M10K	possibly damaging	Het
C1s2	T	C	6: 124,602,649 (GRCm39)	K515E	probably benign	Het
Cars1	A	T	7: 143,123,587 (GRCm39)	Y455N	probably damaging	Het
Ccdc110	A	G	8: 46,396,460 (GRCm39)	S784G	probably benign	Het
Chic2	A	G	5: 75,171,872 (GRCm39)		probably benign	Het
Chka	A	T	19: 3,942,105 (GRCm39)		probably null	Het
Chrne	A	G	11: 70,506,101 (GRCm39)	I420T	possibly damaging	Het
Cobll1	A	G	2: 64,929,602 (GRCm39)	S575P	possibly damaging	Het
Col6a6	A	T	9: 105,666,147 (GRCm39)	L3Q	probably damaging	Het
Comtd1	A	T	14: 21,898,813 (GRCm39)		probably benign	Het
Cpsf2	T	C	12: 101,948,243 (GRCm39)	V13A	probably benign	Het
Creb3l4	T	A	3: 90,149,521 (GRCm39)	I115L	probably benign	Het
Cyp2j12	C	T	4: 95,990,346 (GRCm39)	A407T	possibly damaging	Het
Ddr2	A	G	1: 169,825,498 (GRCm39)		probably null	Het
Dennd4c	T	C	4: 86,725,775 (GRCm39)	L743P	probably damaging	Het
Egfl8	T	C	17: 34,833,171 (GRCm39)	T192A	probably benign	Het
Elapor1	C	T	3: 108,379,284 (GRCm39)		probably null	Het
Elf3	A	G	1: 135,184,473 (GRCm39)		probably benign	Het
Entrep2	A	G	7: 64,417,439 (GRCm39)	S322P	probably benign	Het
Etv3	T	G	3: 87,443,223 (GRCm39)	L269R	possibly damaging	Het
Fah	C	A	7: 84,251,260 (GRCm39)		probably benign	Het
Fbll1	C	A	11: 35,688,407 (GRCm39)	L285F	probably benign	Het
Fcrla	A	T	1: 170,748,682 (GRCm39)	F154I	probably damaging	Het
Fnip2	T	A	3: 79,396,701 (GRCm39)		probably null	Het
Focad	T	C	4: 88,115,083 (GRCm39)		probably benign	Het
Gabrr1	T	A	4: 33,162,820 (GRCm39)	I462N	possibly damaging	Het
Gm57859	C	A	11: 113,579,805 (GRCm39)	T400K	probably benign	Het
Gnptab	A	G	10: 88,265,485 (GRCm39)	T366A	probably benign	Het
Hnrnpu	G	A	1: 178,159,017 (GRCm39)		probably benign	Het
Il17ra	T	A	6: 120,454,406 (GRCm39)	V299E	possibly damaging	Het
Impg1	G	A	9: 80,252,360 (GRCm39)	Q607*	probably null	Het
Impg1	T	A	9: 80,252,827 (GRCm39)	E374V	probably damaging	Het
Itgax	C	T	7: 127,747,700 (GRCm39)	L1039F	probably benign	Het
Kcnk2	A	T	1: 189,072,133 (GRCm39)	V65D	probably damaging	Het
Kif20b	A	C	19: 34,918,611 (GRCm39)		probably null	Het
Krt9	TCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCC	TCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCCCCCACTTCCTCCTCCATAGCTGCC	11: 100,079,903 (GRCm39)		probably benign	Het
Lama5	T	G	2: 179,825,942 (GRCm39)	I2372L	probably benign	Het
Lilrb4a	A	G	10: 51,368,139 (GRCm39)	T85A	possibly damaging	Het
Mapk13	C	A	17: 28,997,197 (GRCm39)	H330N	probably benign	Het
Mars1	C	A	10: 127,132,549 (GRCm39)		probably benign	Het
Mdga1	C	A	17: 30,057,052 (GRCm39)	R818L	probably damaging	Het
Mdn1	T	A	4: 32,671,608 (GRCm39)	L476Q	possibly damaging	Het
Mup21	T	C	4: 62,066,202 (GRCm39)	E178G	probably benign	Het
Myg1	A	G	15: 102,240,288 (GRCm39)	N38S	probably benign	Het
Ncam1	A	T	9: 49,416,779 (GRCm39)	D837E	probably benign	Het
Ncam2	C	T	16: 81,386,679 (GRCm39)	P686L	possibly damaging	Het
Nck2	T	C	1: 43,500,231 (GRCm39)		probably benign	Het
Nfya	T	C	17: 48,707,563 (GRCm39)		probably benign	Het
Npat	A	G	9: 53,482,330 (GRCm39)	K1346R	probably damaging	Het
Odad2	C	G	18: 7,181,787 (GRCm39)	D846H	probably damaging	Het
Or12j3	G	T	7: 139,952,920 (GRCm39)	T201K	probably benign	Het
Or4a72	T	C	2: 89,406,023 (GRCm39)	T16A	probably damaging	Het
Or6c212	A	G	10: 129,558,681 (GRCm39)	V244A	probably benign	Het
Pde7b	G	T	10: 20,288,873 (GRCm39)	Q325K	probably damaging	Het
Pla2r1	A	T	2: 60,253,056 (GRCm39)	M1345K	probably benign	Het
Prkcz	T	C	4: 155,441,946 (GRCm39)	D62G	probably damaging	Het
Pros1	T	A	16: 62,723,935 (GRCm39)	C228S	possibly damaging	Het
Ptprc	A	G	1: 138,006,236 (GRCm39)	M782T	possibly damaging	Het
Rcn1	T	C	2: 105,219,518 (GRCm39)	D225G	probably benign	Het
Recql4	G	A	15: 76,594,381 (GRCm39)	R46C	probably damaging	Het
Rnf220	C	T	4: 117,346,797 (GRCm39)	R205Q	possibly damaging	Het
Samd13	T	C	3: 146,368,502 (GRCm39)	D11G	probably benign	Het
Scp2d1	T	A	2: 144,666,030 (GRCm39)	I123K	probably benign	Het
Skap1	A	T	11: 96,644,870 (GRCm39)	Y311F	probably damaging	Het
Slc2a10	T	C	2: 165,356,676 (GRCm39)	I112T	possibly damaging	Het
Slc34a1	G	A	13: 24,003,078 (GRCm39)	V243M	probably benign	Het
Slc39a2	G	A	14: 52,132,711 (GRCm39)	G218D	probably damaging	Het
Sos1	T	C	17: 80,742,381 (GRCm39)	N382S	probably benign	Het
Spam1	C	T	6: 24,796,655 (GRCm39)	T202I	probably damaging	Het
Tas2r138	T	A	6: 40,589,820 (GRCm39)	Q142L	possibly damaging	Het
Tec	T	A	5: 72,939,365 (GRCm39)	R217*	probably null	Het
Tmeff2	T	A	1: 50,969,804 (GRCm39)	V90D	probably benign	Het
Tmem119	T	C	5: 113,933,405 (GRCm39)	Y132C	probably damaging	Het
Topbp1	A	G	9: 103,190,035 (GRCm39)	I204V	probably benign	Het
Trappc14	A	T	5: 138,260,641 (GRCm39)		probably benign	Het
Ttn	A	T	2: 76,601,232 (GRCm39)	I17001N	probably damaging	Het
Vit	T	A	17: 78,894,270 (GRCm39)	M224K	probably benign	Het
Vmn1r179	T	G	7: 23,628,491 (GRCm39)	H227Q	possibly damaging	Het
Vmn1r84	T	C	7: 12,095,743 (GRCm39)	N305D	probably benign	Het
Vmn2r61	A	G	7: 41,916,520 (GRCm39)	N378D	probably damaging	Het
Vmn2r87	A	G	10: 130,314,435 (GRCm39)	Y384H	probably damaging	Het
Wiz	C	T	17: 32,580,570 (GRCm39)	A294T	probably benign	Het
Xdh	C	A	17: 74,231,931 (GRCm39)	V260L	possibly damaging	Het
Xirp2	A	G	2: 67,343,237 (GRCm39)	K1826R	probably benign	Het
Zfp445	A	C	9: 122,681,358 (GRCm39)	I861R	probably benign	Het
Zfp691	T	C	4: 119,027,999 (GRCm39)	T78A	probably benign	Het

Other mutations in Clstn1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00486:Clstn1	APN	4	149,719,700 (GRCm39)	missense	probably damaging	0.99
IGL00585:Clstn1	APN	4	149,722,769 (GRCm39)	missense	probably benign	0.05
IGL00911:Clstn1	APN	4	149,727,648 (GRCm39)	splice site	probably benign
IGL01394:Clstn1	APN	4	149,719,239 (GRCm39)	missense	possibly damaging	0.87
IGL02193:Clstn1	APN	4	149,729,809 (GRCm39)	missense	probably benign	0.03
IGL02406:Clstn1	APN	4	149,711,816 (GRCm39)	missense	probably damaging	1.00
IGL02501:Clstn1	APN	4	149,716,299 (GRCm39)	missense	probably damaging	1.00
IGL02641:Clstn1	APN	4	149,713,968 (GRCm39)	missense	probably null	1.00
R0012:Clstn1	UTSW	4	149,719,253 (GRCm39)	missense	probably damaging	0.96
R0020:Clstn1	UTSW	4	149,719,253 (GRCm39)	missense	probably damaging	0.96
R0021:Clstn1	UTSW	4	149,719,253 (GRCm39)	missense	probably damaging	0.96
R0026:Clstn1	UTSW	4	149,719,253 (GRCm39)	missense	probably damaging	0.96
R0031:Clstn1	UTSW	4	149,719,253 (GRCm39)	missense	probably damaging	0.96
R0038:Clstn1	UTSW	4	149,719,253 (GRCm39)	missense	probably damaging	0.96
R0062:Clstn1	UTSW	4	149,719,253 (GRCm39)	missense	probably damaging	0.96
R0064:Clstn1	UTSW	4	149,719,253 (GRCm39)	missense	probably damaging	0.96
R0193:Clstn1	UTSW	4	149,719,253 (GRCm39)	missense	probably damaging	0.96
R0279:Clstn1	UTSW	4	149,728,131 (GRCm39)	missense	probably damaging	1.00
R0394:Clstn1	UTSW	4	149,728,635 (GRCm39)	missense	probably benign	0.00
R0609:Clstn1	UTSW	4	149,713,757 (GRCm39)	splice site	probably null
R0685:Clstn1	UTSW	4	149,731,312 (GRCm39)	missense	probably benign	0.24
R0724:Clstn1	UTSW	4	149,728,081 (GRCm39)	missense	possibly damaging	0.84
R1016:Clstn1	UTSW	4	149,731,286 (GRCm39)	missense	probably benign	0.21
R1470:Clstn1	UTSW	4	149,719,179 (GRCm39)	missense	possibly damaging	0.94
R1470:Clstn1	UTSW	4	149,719,179 (GRCm39)	missense	possibly damaging	0.94
R1622:Clstn1	UTSW	4	149,713,864 (GRCm39)	missense	probably damaging	0.97
R1680:Clstn1	UTSW	4	149,728,183 (GRCm39)	missense	probably benign	0.02
R3803:Clstn1	UTSW	4	149,719,796 (GRCm39)	missense	probably damaging	0.99
R3836:Clstn1	UTSW	4	149,722,790 (GRCm39)	missense	probably damaging	1.00
R3838:Clstn1	UTSW	4	149,722,790 (GRCm39)	missense	probably damaging	1.00
R5024:Clstn1	UTSW	4	149,719,751 (GRCm39)	missense	possibly damaging	0.91
R5919:Clstn1	UTSW	4	149,719,703 (GRCm39)	missense	probably damaging	1.00
R6269:Clstn1	UTSW	4	149,728,524 (GRCm39)	missense	probably benign	0.00
R6354:Clstn1	UTSW	4	149,727,673 (GRCm39)	missense	probably benign	0.05
R6382:Clstn1	UTSW	4	149,710,577 (GRCm39)	splice site	probably null
R6573:Clstn1	UTSW	4	149,728,146 (GRCm39)	missense	probably damaging	1.00
R7342:Clstn1	UTSW	4	149,713,887 (GRCm39)	missense	probably damaging	0.98
R7457:Clstn1	UTSW	4	149,719,373 (GRCm39)	missense	probably benign	0.03
R7571:Clstn1	UTSW	4	149,730,744 (GRCm39)	missense	probably benign	0.38
R7682:Clstn1	UTSW	4	149,710,558 (GRCm39)	missense	possibly damaging	0.72
R7738:Clstn1	UTSW	4	149,719,811 (GRCm39)	missense	probably damaging	1.00
R7803:Clstn1	UTSW	4	149,716,328 (GRCm39)	missense	probably damaging	1.00
R7904:Clstn1	UTSW	4	149,698,594 (GRCm39)	missense	probably benign	0.01
R7918:Clstn1	UTSW	4	149,728,508 (GRCm39)	missense	probably damaging	0.98
R8007:Clstn1	UTSW	4	149,716,305 (GRCm39)	missense	probably damaging	1.00
R8821:Clstn1	UTSW	4	149,730,780 (GRCm39)	missense	probably benign	0.00
R8831:Clstn1	UTSW	4	149,730,780 (GRCm39)	missense	probably benign	0.00
R9169:Clstn1	UTSW	4	149,731,322 (GRCm39)	missense	possibly damaging	0.68
R9173:Clstn1	UTSW	4	149,710,564 (GRCm39)	missense	probably benign	0.08
R9463:Clstn1	UTSW	4	149,698,564 (GRCm39)	missense	possibly damaging	0.92
R9491:Clstn1	UTSW	4	149,731,929 (GRCm39)	missense	probably damaging	1.00
R9615:Clstn1	UTSW	4	149,722,757 (GRCm39)	missense	probably damaging	1.00
X0020:Clstn1	UTSW	4	149,719,708 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TATGTCACCTGCAGCCTCTG -3'
(R):5'- TAAAGCAAAGCAAGCAGGCATTTC -3'

Sequencing Primer
(F):5'- GCCTCTGCTATTTCTGGTCTC -3'
(R):5'- ATTTCTCCATCCTGGGGCATGAG -3'

Posted On

2016-04-15