Mutagenetix > Incidental Mutation

Incidental Mutation 'R7483:Sdcbp'

579894

Institutional Source

Beutler Lab

Gene Symbol

Sdcbp

Ensembl Gene

ENSMUSG00000028249

Gene Name

syndecan binding protein

Synonyms

syntenin-1, Sycl, MDA-9, syndecan interacting protein, syntenin

MMRRC Submission

045557-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.166) question?

Stock #

R7483 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

6365654-6396122 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 6393089 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 242 (I242T)

Ref Sequence

ENSEMBL: ENSMUSP00000029912 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029910] [ENSMUST00000029912] [ENSMUST00000103008] [ENSMUST00000108374] [ENSMUST00000153861] [ENSMUST00000175769]

AlphaFold

O08992

Predicted Effect

probably benign
Transcript: ENSMUST00000029910

SMART Domains

Protein: ENSMUSP00000029910
Gene: ENSMUSG00000028245

Domain	Start	End	E-Value	Type
low complexity region	23	28	N/A	INTRINSIC
GRAM	176	247	2.22e-11	SMART
Beach	302	575	6.28e-190	SMART
WD40	622	661	4.55e-3	SMART
WD40	664	703	2.97e0	SMART
WD40	706	743	1.47e-6	SMART
WD40	756	794	1.7e-2	SMART
WD40	797	836	1.02e-5	SMART
WD40	839	875	9.55e0	SMART
WD40	878	917	1.5e-3	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000029912
AA Change: I242T

PolyPhen 2 Score 0.952 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000029912
Gene: ENSMUSG00000028249
AA Change: I242T

Domain	Start	End	E-Value	Type
PDZ	124	195	7.09e-15	SMART
PDZ	208	274	6.04e-9	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000103008
AA Change: I241T

PolyPhen 2 Score 0.952 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000100073
Gene: ENSMUSG00000028249
AA Change: I241T

Domain	Start	End	E-Value	Type
PDZ	123	194	7.09e-15	SMART
PDZ	207	273	6.04e-9	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000108374

SMART Domains

Protein: ENSMUSP00000104011
Gene: ENSMUSG00000028249

Domain	Start	End	E-Value	Type
PDZ	124	195	2.84e-14	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000153861

SMART Domains

Protein: ENSMUSP00000119838
Gene: ENSMUSG00000028249

Domain	Start	End	E-Value	Type
PDZ	123	194	7.09e-15	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000175769
AA Change: I242T

PolyPhen 2 Score 0.952 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000135777
Gene: ENSMUSG00000028249
AA Change: I242T

Domain	Start	End	E-Value	Type
PDZ	124	195	7.09e-15	SMART
Blast:PDZ	208	249	1e-21	BLAST

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene was initially identified as a molecule linking syndecan-mediated signaling to the cytoskeleton. The syntenin protein contains tandemly repeated PDZ domains that bind the cytoplasmic, C-terminal domains of a variety of transmembrane proteins. This protein may also affect cytoskeletal-membrane organization, cell adhesion, protein trafficking, and the activation of transcription factors. The protein is primarily localized to membrane-associated adherens junctions and focal adhesions but is also found at the endoplasmic reticulum and nucleus. Alternative splicing results in multiple transcript variants encoding different isoforms. Related pseudogenes have been identified on multiple chromosomes. [provided by RefSeq, Jan 2017]
PHENOTYPE: Mice heterozygous for a conditional allele activated in neurons exhibit abnormal dendrite morphology and reduced mEPSC frequency. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acad10	A	T	5: 121,794,075 (GRCm39)		probably null	Het
Ahnak	T	C	19: 8,982,186 (GRCm39)	S1157P	probably damaging	Het
Akap12	T	G	10: 4,303,967 (GRCm39)	V364G	probably benign	Het
Ankrd17	A	G	5: 90,447,855 (GRCm39)	S229P	probably benign	Het
Apof	A	T	10: 128,104,636 (GRCm39)	Y5F	probably benign	Het
Arhgap24	T	A	5: 102,989,174 (GRCm39)	M94K	probably benign	Het
Ash2l	G	T	8: 26,312,798 (GRCm39)	D479E	probably damaging	Het
Atp8a2	A	T	14: 60,245,824 (GRCm39)	C623S	probably benign	Het
Bmper	T	A	9: 23,395,238 (GRCm39)	N656K	probably benign	Het
Braf	T	C	6: 39,604,772 (GRCm39)	I619V	possibly damaging	Het
Brwd1	T	C	16: 95,857,373 (GRCm39)	R396G	probably damaging	Het
Car7	A	T	8: 105,276,216 (GRCm39)	T234S	probably benign	Het
Catsper4	A	T	4: 133,945,552 (GRCm39)	V169E	probably damaging	Het
Cemip	T	G	7: 83,647,784 (GRCm39)	I99L	probably damaging	Het
Chrna7	C	A	7: 62,754,738 (GRCm39)	V290L	probably damaging	Het
Clip1	A	T	5: 123,755,447 (GRCm39)	D944E	probably benign	Het
Cplane2	A	G	4: 140,947,153 (GRCm39)	D178G	probably damaging	Het
Cyp2c68	T	C	19: 39,677,581 (GRCm39)	T470A	probably benign	Het
Dmbx1	G	T	4: 115,780,908 (GRCm39)	A31D	probably damaging	Het
Dnah7b	T	C	1: 46,214,579 (GRCm39)	F1115L	probably damaging	Het
Dock10	T	C	1: 80,493,283 (GRCm39)	I1897V	probably benign	Het
Efcab3	A	G	11: 105,000,112 (GRCm39)	I234V	probably benign	Het
Eid2b	T	G	7: 27,977,243 (GRCm39)	L13R	probably damaging	Het
Enam	A	G	5: 88,649,679 (GRCm39)	Y396C	probably damaging	Het
Fam161a	A	T	11: 22,971,006 (GRCm39)	T395S	probably damaging	Het
Fat1	A	G	8: 45,476,197 (GRCm39)	R1748G	probably benign	Het
Fdxacb1	C	A	9: 50,681,451 (GRCm39)	T124K	possibly damaging	Het
Fer1l6	A	T	15: 58,513,794 (GRCm39)	D1563V	possibly damaging	Het
Gm20834	T	C	Y: 10,323,226 (GRCm39)	H70R	probably damaging	Het
Gucy2d	T	A	7: 98,098,964 (GRCm39)	M261K	probably damaging	Het
Hcar2	T	A	5: 124,002,861 (GRCm39)	Q214L	probably benign	Het
Hdac11	C	T	6: 91,136,214 (GRCm39)	H75Y	probably damaging	Het
Hoxa2	C	A	6: 52,141,279 (GRCm39)	A116S	probably benign	Het
Ints2	A	G	11: 86,106,444 (GRCm39)	C989R	probably damaging	Het
Jpt1	T	C	11: 115,393,950 (GRCm39)	E36G	probably damaging	Het
Kdm5d	G	A	Y: 914,044 (GRCm39)	R327Q	possibly damaging	Het
Klhl1	T	C	14: 96,584,304 (GRCm39)	M309V	probably benign	Het
Larp4	A	G	15: 99,889,659 (GRCm39)	K193E	probably benign	Het
Lmo3	C	T	6: 138,393,500 (GRCm39)	C40Y	probably damaging	Het
Mcm4	A	G	16: 15,448,306 (GRCm39)	V417A	probably benign	Het
Med8	A	G	4: 118,268,176 (GRCm39)	E34G	probably damaging	Het
Mex3b	G	T	7: 82,517,114 (GRCm39)	A86S	possibly damaging	Het
Muc6	T	C	7: 141,224,245 (GRCm39)	T1646A	unknown	Het
Myo15b	A	T	11: 115,749,570 (GRCm39)	E113D		Het
Myo7a	T	A	7: 97,712,881 (GRCm39)	H1698L	probably benign	Het
Myocos	T	A	1: 162,484,678 (GRCm39)	M44L	unknown	Het
Nalcn	A	G	14: 123,551,499 (GRCm39)	V1036A	probably damaging	Het
Nfrkb	C	T	9: 31,325,328 (GRCm39)	Q924*	probably null	Het
Nol6	A	G	4: 41,117,424 (GRCm39)	L923P	possibly damaging	Het
Nrxn3	T	C	12: 89,477,232 (GRCm39)	Y472H	probably damaging	Het
Nudcd1	A	G	15: 44,269,253 (GRCm39)	Y136H	possibly damaging	Het
Obox2	T	C	7: 15,131,241 (GRCm39)	C116R	probably damaging	Het
Onecut3	A	T	10: 80,331,310 (GRCm39)	S157C	unknown	Het
Or10ak11	A	G	4: 118,687,517 (GRCm39)	V39A	probably damaging	Het
Or11g27	T	A	14: 50,771,472 (GRCm39)	V201D	probably benign	Het
Or2d2b	T	A	7: 106,705,982 (GRCm39)	I29F	probably benign	Het
Or4f15	T	C	2: 111,814,124 (GRCm39)	I98M	probably damaging	Het
Oscp1	C	T	4: 125,967,726 (GRCm39)	R91*	probably null	Het
Pclo	A	T	5: 14,762,606 (GRCm39)	D408V		Het
Pde8a	T	C	7: 80,932,581 (GRCm39)	V81A	probably benign	Het
Pde8b	T	A	13: 95,164,251 (GRCm39)	D653V	probably damaging	Het
Peg10	T	TCCG	6: 4,756,451 (GRCm39)		probably benign	Het
Pik3cg	T	C	12: 32,245,647 (GRCm39)	Y867C	probably damaging	Het
Pkd1l3	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	8: 110,350,827 (GRCm39)		probably benign	Het
Psd4	A	T	2: 24,294,768 (GRCm39)	D776V	possibly damaging	Het
Ptprb	A	G	10: 116,119,334 (GRCm39)	E156G	probably benign	Het
Rad54b	A	G	4: 11,610,372 (GRCm39)	Y663C	probably damaging	Het
Ranbp3l	T	A	15: 9,030,955 (GRCm39)	V78D	possibly damaging	Het
Rbm12	T	C	2: 155,940,138 (GRCm39)	I45V	unknown	Het
Scn9a	A	G	2: 66,363,692 (GRCm39)	V862A	probably damaging	Het
Slc25a24	A	G	3: 109,066,751 (GRCm39)	T302A	probably damaging	Het
Slc45a3	G	T	1: 131,904,549 (GRCm39)		probably benign	Het
Srpk1	T	C	17: 28,813,192 (GRCm39)	I517M	probably benign	Het
Tmx4	A	G	2: 134,481,581 (GRCm39)	M114T	probably benign	Het
Trhr	T	A	15: 44,092,627 (GRCm39)	V288D	probably damaging	Het
Tspoap1	A	T	11: 87,652,351 (GRCm39)	I42F	probably benign	Het
Ttn	A	T	2: 76,781,856 (GRCm39)	D1063E	unknown	Het
Tusc3	A	G	8: 39,538,635 (GRCm39)	I225V	probably benign	Het
Ugt2b38	A	G	5: 87,571,973 (GRCm39)	S20P	probably damaging	Het
Upf2	A	G	2: 6,032,219 (GRCm39)	T922A	unknown	Het
Usp38	C	T	8: 81,741,190 (GRCm39)		probably benign	Het
Vmn1r216	A	G	13: 23,283,738 (GRCm39)	I140M	probably damaging	Het
Vmn2r115	T	A	17: 23,565,371 (GRCm39)	N419K	possibly damaging	Het
Vmn2r55	C	T	7: 12,404,755 (GRCm39)	G216D	probably benign	Het
Vwa8	A	C	14: 79,219,674 (GRCm39)		probably null	Het
Wnt7b	C	A	15: 85,421,615 (GRCm39)	R349L	possibly damaging	Het
Xbp1	T	C	11: 5,471,098 (GRCm39)	V35A	probably benign	Het
Zan	A	T	5: 137,445,057 (GRCm39)	M1734K	unknown	Het
Zfhx4	A	G	3: 5,477,237 (GRCm39)	E3284G	probably damaging	Het
Zfp458	A	G	13: 67,404,978 (GRCm39)	L487S	possibly damaging	Het
Zfp687	C	T	3: 94,914,841 (GRCm39)	R1220H	probably damaging	Het
Zp1	A	G	19: 10,895,280 (GRCm39)	L324P	possibly damaging	Het

Other mutations in Sdcbp

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00983:Sdcbp	APN	4	6,392,953 (GRCm39)	nonsense	probably null
R0158:Sdcbp	UTSW	4	6,379,042 (GRCm39)	missense	possibly damaging	0.81
R1066:Sdcbp	UTSW	4	6,385,120 (GRCm39)	missense	probably damaging	0.98
R1115:Sdcbp	UTSW	4	6,377,143 (GRCm39)	critical splice donor site	probably null
R1353:Sdcbp	UTSW	4	6,381,057 (GRCm39)	missense	probably damaging	0.99
R2006:Sdcbp	UTSW	4	6,386,536 (GRCm39)	missense	probably benign	0.23
R4879:Sdcbp	UTSW	4	6,381,056 (GRCm39)	missense	possibly damaging	0.93
R4979:Sdcbp	UTSW	4	6,378,980 (GRCm39)	nonsense	probably null
R5034:Sdcbp	UTSW	4	6,393,118 (GRCm39)	critical splice donor site	probably null
R5072:Sdcbp	UTSW	4	6,393,019 (GRCm39)	missense	probably benign	0.07
R6307:Sdcbp	UTSW	4	6,385,059 (GRCm39)	missense	probably benign	0.06
R6329:Sdcbp	UTSW	4	6,381,064 (GRCm39)	missense	probably benign	0.04
R7665:Sdcbp	UTSW	4	6,385,144 (GRCm39)	missense	probably benign	0.11
R7722:Sdcbp	UTSW	4	6,385,063 (GRCm39)	missense	possibly damaging	0.93
R7729:Sdcbp	UTSW	4	6,378,985 (GRCm39)	missense	probably benign	0.06
R7807:Sdcbp	UTSW	4	6,393,688 (GRCm39)	missense	probably damaging	1.00
R8025:Sdcbp	UTSW	4	6,393,022 (GRCm39)	missense	probably benign	0.09
R8941:Sdcbp	UTSW	4	6,393,661 (GRCm39)	missense	probably benign	0.22
R9093:Sdcbp	UTSW	4	6,386,709 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- TCCCATGTGGCAGAGTTTG -3'
(R):5'- CAGAATGTCTAAATATTTCCCTGCC -3'

Sequencing Primer
(F):5'- AGGTATGTCATGTCTATTGAAACATG -3'
(R):5'- GTCCTGCCACCTAAATGA -3'

Posted On

2019-10-07