Mutagenetix > Incidental Mutation

Incidental Mutation 'R5024:Clstn1'

391213

Institutional Source

Beutler Lab

Gene Symbol

Clstn1

Ensembl Gene

ENSMUSG00000039953

Gene Name

calsyntenin 1

Synonyms

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

MMRRC Submission

042615-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5024 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

149670925-149733356 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 149719751 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Histidine at position 432 (R432H)

Ref Sequence

ENSEMBL: ENSMUSP00000036962 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000039144] [ENSMUST00000105691]

AlphaFold

Q9EPL2

Predicted Effect

possibly damaging
Transcript: ENSMUST00000039144
AA Change: R432H

PolyPhen 2 Score 0.910 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000036962
Gene: ENSMUSG00000039953
AA Change: R432H

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: ENSMUST00000105691
AA Change: R422H

PolyPhen 2 Score 0.228 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000101316
Gene: ENSMUSG00000039953
AA Change: R422H

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

noncoding transcript
Transcript: ENSMUST00000151895

Meta Mutation Damage Score

0.5788

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.6%
20x: 93.4%

Validation Efficiency

99% (95/96)

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: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrd1	A	G	5: 129,248,959 (GRCm39)	N575S	probably damaging	Het
Akap6	C	T	12: 53,189,345 (GRCm39)	T2253M	probably benign	Het
Arhgef37	A	C	18: 61,639,511 (GRCm39)	N289K	probably damaging	Het
Atad2b	A	C	12: 4,987,534 (GRCm39)	T121P	probably benign	Het
Atp4a	A	C	7: 30,415,289 (GRCm39)	D303A	possibly damaging	Het
Calu	A	T	6: 29,374,518 (GRCm39)		probably benign	Het
Ccdc141	A	C	2: 76,885,047 (GRCm39)	N531K	probably benign	Het
Ccdc146	T	C	5: 21,604,612 (GRCm39)		probably null	Het
Cd207	G	A	6: 83,651,301 (GRCm39)	T218I	probably damaging	Het
Cd2ap	A	C	17: 43,116,236 (GRCm39)		probably null	Het
Ceacam23	A	G	7: 17,644,607 (GRCm39)	I575V	probably benign	Het
Clip3	G	A	7: 29,991,644 (GRCm39)		probably benign	Het
Csmd2	A	G	4: 128,215,141 (GRCm39)	Y521C	possibly damaging	Het
Dnah8	A	T	17: 30,955,070 (GRCm39)	E2033V	probably damaging	Het
Eng	T	G	2: 32,563,404 (GRCm39)	V319G	probably benign	Het
Erp44	C	T	4: 48,241,296 (GRCm39)	W57*	probably null	Het
Etv1	T	A	12: 38,904,233 (GRCm39)		probably null	Het
Eva1c	T	C	16: 90,673,081 (GRCm39)		probably null	Het
Fam221b	T	A	4: 43,659,674 (GRCm39)	N482I	probably damaging	Het
Fam83h	T	C	15: 75,876,991 (GRCm39)	H202R	probably damaging	Het
Fbxw13	T	C	9: 109,008,403 (GRCm39)	T449A	probably benign	Het
Fbxw25	A	T	9: 109,492,442 (GRCm39)		probably null	Het
Frmd3	T	A	4: 74,016,381 (GRCm39)	S99T	probably benign	Het
Gm5174	G	T	10: 86,492,451 (GRCm39)		noncoding transcript	Het
Gm815	C	T	19: 26,865,175 (GRCm39)	Q49*	probably null	Het
H2-DMa	A	T	17: 34,357,461 (GRCm39)	I245F	possibly damaging	Het
Herc1	A	T	9: 66,377,608 (GRCm39)	K3458M	possibly damaging	Het
Hirip3	A	G	7: 126,463,661 (GRCm39)		probably null	Het
Hjurp	A	T	1: 88,202,772 (GRCm39)	Y71N	possibly damaging	Het
Hmcn1	T	A	1: 150,556,439 (GRCm39)	E2449V	possibly damaging	Het
Igll1	G	T	16: 16,681,657 (GRCm39)	H33N	probably benign	Het
Il6	T	C	5: 30,224,512 (GRCm39)	L184P	probably damaging	Het
Impg2	T	A	16: 56,080,463 (GRCm39)	S756T	probably damaging	Het
Insyn2a	A	G	7: 134,520,207 (GRCm39)	S108P	probably damaging	Het
Kank4	T	G	4: 98,673,898 (GRCm39)	D5A	probably damaging	Het
Kcna7	G	A	7: 45,056,015 (GRCm39)	R77H	probably damaging	Het
Kcns2	A	T	15: 34,839,683 (GRCm39)	T349S	probably benign	Het
Keap1	A	G	9: 21,148,522 (GRCm39)	Y162H	probably damaging	Het
Kif9	T	C	9: 110,312,161 (GRCm39)	F10L	possibly damaging	Het
Klhdc8b	ACACGCACGCACGCACGCACGCACGCACGCACGCACGCAC	ACACGCACGCACGCACGCACGCACGCACGCACGCACGCACGCAC	9: 108,326,184 (GRCm39)		probably benign	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Lpar6	A	G	14: 73,476,809 (GRCm39)	T257A	probably damaging	Het
Lpin1	A	T	12: 16,604,007 (GRCm39)	L608Q	probably benign	Het
Lyst	T	C	13: 13,808,989 (GRCm39)	S220P	probably benign	Het
M1ap	A	G	6: 83,005,339 (GRCm39)		probably benign	Het
Mbd6	C	T	10: 127,122,310 (GRCm39)	V173I	probably benign	Het
Myo5b	A	T	18: 74,849,105 (GRCm39)	T1115S	possibly damaging	Het
Mysm1	C	A	4: 94,839,253 (GRCm39)	V683F	possibly damaging	Het
Nlrp4g	T	A	9: 124,350,155 (GRCm38)		noncoding transcript	Het
Odad2	T	C	18: 7,088,555 (GRCm39)	M1005V	probably benign	Het
Or14c39	A	T	7: 86,344,089 (GRCm39)	M142L	probably benign	Het
Or2ak5	T	A	11: 58,611,776 (GRCm39)	I33F	probably benign	Het
Or5al6	G	T	2: 85,976,877 (GRCm39)	A67E	probably damaging	Het
Or8j3c	C	T	2: 86,253,805 (GRCm39)	G72S	possibly damaging	Het
Otud6b	T	A	4: 14,826,293 (GRCm39)	Q34L	probably damaging	Het
Parp11	C	T	6: 127,448,599 (GRCm39)	T72I	probably damaging	Het
Pbx1	T	A	1: 168,011,158 (GRCm39)	D343V	possibly damaging	Het
Phf11	T	C	14: 59,495,932 (GRCm39)		probably null	Het
Ppp1r12b	G	T	1: 134,883,471 (GRCm39)	A17E	probably benign	Het
Pramel15	C	A	4: 144,099,878 (GRCm39)	E296*	probably null	Het
Ranbp9	A	T	13: 43,588,331 (GRCm39)	I67N	probably damaging	Het
Rasgrp4	A	G	7: 28,847,832 (GRCm39)	E414G	probably damaging	Het
Rbbp5	A	G	1: 132,418,226 (GRCm39)	H15R	possibly damaging	Het
Scd2	A	G	19: 44,289,710 (GRCm39)	Y235C	probably benign	Het
Sdr16c5	C	T	4: 4,010,365 (GRCm39)	G170S	probably damaging	Het
Sh3bp4	G	T	1: 89,073,317 (GRCm39)	G722C	probably damaging	Het
Shmt1	A	T	11: 60,688,305 (GRCm39)		probably benign	Het
Slc12a1	A	G	2: 125,008,057 (GRCm39)	I206V	probably benign	Het
Slc26a3	A	G	12: 31,503,907 (GRCm39)	D304G	probably benign	Het
Slc26a7	T	A	4: 14,532,572 (GRCm39)	D434V	possibly damaging	Het
Slc6a16	G	T	7: 44,909,390 (GRCm39)	M185I	probably benign	Het
Stat4	A	G	1: 52,121,729 (GRCm39)	I363V	possibly damaging	Het
Tgfb1i1	G	T	7: 127,847,389 (GRCm39)	M1I	probably null	Het
Thoc2l	A	G	5: 104,670,124 (GRCm39)	K1549E	possibly damaging	Het
Tmem225	T	C	9: 40,060,639 (GRCm39)	V66A	probably benign	Het
Tmtc4	T	C	14: 123,178,714 (GRCm39)		probably null	Het
Trpc4	T	A	3: 54,102,217 (GRCm39)	N38K	probably benign	Het
Ttll12	A	T	15: 83,471,314 (GRCm39)	Y218N	probably damaging	Het
Ttn	A	T	2: 76,778,769 (GRCm39)		probably null	Het
Tulp1	A	C	17: 28,570,969 (GRCm39)	Y178*	probably null	Het
Vmn2r58	A	G	7: 41,513,746 (GRCm39)	V299A	probably damaging	Het
Washc4	C	A	10: 83,419,200 (GRCm39)	Q911K	possibly damaging	Het
Wdr3	T	C	3: 100,062,252 (GRCm39)	D221G	probably benign	Het
Zan	A	T	5: 137,460,155 (GRCm39)	C1245*	probably null	Het
Zfyve9	A	C	4: 108,548,866 (GRCm39)	S773A	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
R4923:Clstn1	UTSW	4	149,729,486 (GRCm39)	missense	probably benign	0.07
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'- TACTCAGTAAAGTGCCCGTG -3'
(R):5'- AAGGAGCTTAAAGAGTCTGATATGCC -3'

Sequencing Primer
(F):5'- AGTAAAGTGCCCGTGTATCC -3'
(R):5'- AGAGTCTGATATGCCATCCTGTGAC -3'

Posted On

2016-06-06