Mutagenetix > Incidental Mutation

Incidental Mutation 'R9169:Clstn1'

696244

Institutional Source

Beutler Lab

Gene Symbol

Clstn1

Ensembl Gene

ENSMUSG00000039953

Gene Name

calsyntenin 1

Synonyms

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

MMRRC Submission

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9169 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

149670925-149733356 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 149731322 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Leucine at position 888 (R888L)

Ref Sequence

ENSEMBL: ENSMUSP00000036962 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038859] [ENSMUST00000039144] [ENSMUST00000105688] [ENSMUST00000105689] [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

possibly damaging
Transcript: ENSMUST00000039144
AA Change: R888L

PolyPhen 2 Score 0.676 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000036962
Gene: ENSMUSG00000039953
AA Change: R888L

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: ENSMUST00000105689

SMART Domains

Protein: ENSMUSP00000101314
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	684	1.35e-84	SMART
PI3Kc	774	1040	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

possibly damaging
Transcript: ENSMUST00000105691
AA Change: R878L

PolyPhen 2 Score 0.783 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000101316
Gene: ENSMUSG00000039953
AA Change: R878L

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

100% (92/92)

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: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610021A01Rik	A	T	7: 41,261,109 (GRCm39)		probably benign	Het
9330182O14Rik	A	T	15: 40,005,632 (GRCm39)	K17*	probably null	Het
Adamtsl3	A	C	7: 82,223,188 (GRCm39)	I990L	probably damaging	Het
Add1	T	A	5: 34,788,122 (GRCm39)	S724T	possibly damaging	Het
Afdn	A	G	17: 14,072,627 (GRCm39)	N865S	probably benign	Het
Amot	A	T	X: 144,244,745 (GRCm39)	L435H		Het
Ap1m2	T	A	9: 21,223,523 (GRCm39)	I8F	probably benign	Het
Atp8a1	T	C	5: 67,824,944 (GRCm39)	T811A		Het
Axin2	A	G	11: 108,822,378 (GRCm39)	D310G	probably damaging	Het
Bin1	T	G	18: 32,562,251 (GRCm39)	F379L	possibly damaging	Het
Bin2	C	A	15: 100,554,631 (GRCm39)	S91I	possibly damaging	Het
Birc5	A	G	11: 117,743,599 (GRCm39)	N111S	probably benign	Het
Blk	T	A	14: 63,620,130 (GRCm39)	N137Y	probably damaging	Het
Cacna1d	G	A	14: 29,796,873 (GRCm39)	A1534V	probably damaging	Het
Cacna2d1	T	C	5: 16,451,757 (GRCm39)	V207A	probably damaging	Het
Ccr3	A	G	9: 123,828,949 (GRCm39)	I95V	probably benign	Het
Celsr2	T	C	3: 108,309,862 (GRCm39)	D1579G	probably benign	Het
Cfap36	C	A	11: 29,196,541 (GRCm39)	K19N	probably benign	Het
Cfap52	C	T	11: 67,844,860 (GRCm39)	V70M	possibly damaging	Het
Chid1	A	T	7: 141,093,722 (GRCm39)	I298N	probably damaging	Het
Col6a5	T	A	9: 105,822,596 (GRCm39)	T254S	unknown	Het
Coro6	C	T	11: 77,359,329 (GRCm39)	P301S	probably damaging	Het
Cstdc2	A	G	2: 148,692,589 (GRCm39)		probably null	Het
Dchs1	T	C	7: 105,422,114 (GRCm39)	D102G	probably damaging	Het
Dnah14	T	C	1: 181,433,381 (GRCm39)	F353L	probably benign	Het
Dnajc10	A	T	2: 80,163,315 (GRCm39)	I344L	probably benign	Het
Dst	T	C	1: 34,303,652 (GRCm39)	V4026A	probably damaging	Het
Exo1	A	G	1: 175,715,203 (GRCm39)	E114G	possibly damaging	Het
Fabp7	A	G	10: 57,662,439 (GRCm39)	I109V	probably benign	Het
Fars2	T	C	13: 36,416,109 (GRCm39)	F206S	probably damaging	Het
Gbp8	C	T	5: 105,179,155 (GRCm39)	A115T	possibly damaging	Het
Gm17067	T	C	7: 42,357,627 (GRCm39)	T292A	probably benign	Het
Gp2	T	C	7: 119,041,929 (GRCm39)	D532G	probably benign	Het
Gtf2i	C	A	5: 134,271,534 (GRCm39)	A917S	probably damaging	Het
Guca1b	A	G	17: 47,702,827 (GRCm39)	E169G	possibly damaging	Het
Hdac1	A	T	4: 129,428,499 (GRCm39)	Y24N	probably damaging	Het
Hepacam	T	C	9: 37,293,693 (GRCm39)	F251L	probably damaging	Het
Hmcn1	G	T	1: 150,506,092 (GRCm39)	N3811K	probably damaging	Het
Htra4	A	T	8: 25,520,133 (GRCm39)	M391K	probably damaging	Het
Ino80d	T	C	1: 63,097,930 (GRCm39)	T760A	probably benign	Het
Ints1	T	G	5: 139,748,586 (GRCm39)	T1074P	probably benign	Het
Itga6	A	T	2: 71,647,015 (GRCm39)	Q75L	possibly damaging	Het
Mapk14	A	C	17: 28,960,814 (GRCm39)	N272T	probably benign	Het
Meikin	A	T	11: 54,285,517 (GRCm39)	T185S	possibly damaging	Het
Moxd2	C	T	6: 40,860,490 (GRCm39)	G318D	possibly damaging	Het
Mtmr3	G	A	11: 4,437,739 (GRCm39)	T905I	probably benign	Het
Muc16	A	G	9: 18,567,824 (GRCm39)	I1565T	unknown	Het
Myh14	A	G	7: 44,271,281 (GRCm39)	S1500P	possibly damaging	Het
Nfkb1	T	C	3: 135,310,874 (GRCm39)	E475G	probably benign	Het
Ngef	C	A	1: 87,473,581 (GRCm39)	R67L	probably benign	Het
Olr1	T	C	6: 129,470,528 (GRCm39)	E213G	probably damaging	Het
Or13c3	T	A	4: 52,856,052 (GRCm39)	I154F	probably damaging	Het
Or5b124	A	G	19: 13,610,903 (GRCm39)	I143V	probably benign	Het
Or8g21	A	G	9: 38,906,573 (GRCm39)	S53P	probably benign	Het
Or9r3	A	C	10: 129,947,723 (GRCm39)	I312R	probably benign	Het
Pcdhga3	C	T	18: 37,809,088 (GRCm39)	L514F	probably damaging	Het
Pcnt	A	G	10: 76,221,572 (GRCm39)	M2018T	possibly damaging	Het
Pde8a	C	T	7: 80,982,619 (GRCm39)	T746I	probably damaging	Het
Pik3ca	T	C	3: 32,503,755 (GRCm39)		probably null	Het
Psapl1	A	G	5: 36,362,880 (GRCm39)	S491G	possibly damaging	Het
Psmf1	A	T	2: 151,577,457 (GRCm39)	D73E	probably benign	Het
Ptprcap	A	G	19: 4,206,358 (GRCm39)	D147G	probably benign	Het
Ramacl	T	C	13: 67,056,063 (GRCm39)	F19L	probably damaging	Het
Rdh8	T	A	9: 20,736,935 (GRCm39)	V309E	possibly damaging	Het
Rhobtb3	T	A	13: 76,041,121 (GRCm39)	T396S	probably benign	Het
Rpa1	A	T	11: 75,200,999 (GRCm39)	L475*	probably null	Het
Rtkn	T	A	6: 83,129,190 (GRCm39)	S562T	probably damaging	Het
Saxo5	A	T	8: 3,525,967 (GRCm39)	Y40F	possibly damaging	Het
Scamp1	C	T	13: 94,389,533 (GRCm39)	D35N	probably benign	Het
Scarb1	C	T	5: 125,371,146 (GRCm39)	A309T	probably damaging	Het
Scube1	G	A	15: 83,543,298 (GRCm39)	T180M	possibly damaging	Het
Sez6	T	G	11: 77,868,473 (GRCm39)	F945V	probably damaging	Het
Sf3a1	C	T	11: 4,116,681 (GRCm39)	T124M	probably benign	Het
Smchd1	T	C	17: 71,722,659 (GRCm39)	K759E	probably damaging	Het
Sort1	C	A	3: 108,247,994 (GRCm39)	C446*	probably null	Het
Sun1	T	A	5: 139,219,273 (GRCm39)	S360T	probably benign	Het
Supv3l1	A	G	10: 62,268,238 (GRCm39)	F536L	probably damaging	Het
Taar6	A	C	10: 23,861,273 (GRCm39)	V91G	probably damaging	Het
Themis	C	A	10: 28,658,233 (GRCm39)	T420N	probably benign	Het
Thoc2l	T	A	5: 104,666,348 (GRCm39)	L290H	probably damaging	Het
Tmc2	T	A	2: 130,083,516 (GRCm39)	I491N	probably damaging	Het
Trmt112	T	C	19: 6,888,187 (GRCm39)	I113T	probably damaging	Het
Ttc14	C	T	3: 33,857,071 (GRCm39)	Q183*	probably null	Het
Txndc16	T	A	14: 45,373,385 (GRCm39)	D748V	probably damaging	Het
Xkr6	A	G	14: 63,844,067 (GRCm39)	D30G	possibly damaging	Het
Zc3h14	C	T	12: 98,745,505 (GRCm39)	S498L	probably damaging	Het
Zc3h7b	A	C	15: 81,661,184 (GRCm39)	D341A	probably benign	Het
Zfp108	T	A	7: 23,960,923 (GRCm39)	C505S	probably damaging	Het
Zfp354c	A	C	11: 50,706,088 (GRCm39)	L329R	probably damaging	Het
Zfyve16	T	A	13: 92,657,871 (GRCm39)	D680V	probably damaging	Het
Znfx1	A	G	2: 166,897,185 (GRCm39)	F580L	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
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
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'- TACCTAGAGTAGTTGAGGAGGCC -3'
(R):5'- TCCTCATCTGAAGGTGACCC -3'

Sequencing Primer
(F):5'- TAGTTGAGGAGGCCAAGGAG -3'
(R):5'- CCCCCTAATCTAATCTCACTGAC -3'

Posted On

2022-02-07