Mutagenetix > Incidental Mutation

Incidental Mutation 'R5072:Sdcbp'

388854

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

Accession Numbers

Essential gene?

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

Stock #

R5072 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

6365654-6396122 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 6393019 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 218 (I218V)

Ref Sequence

ENSEMBL: ENSMUSP00000100073 (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

probably benign
Transcript: ENSMUST00000029912
AA Change: I219V

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000029912
Gene: ENSMUSG00000028249
AA Change: I219V

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

Predicted Effect

probably benign
Transcript: ENSMUST00000103008
AA Change: I218V

PolyPhen 2 Score 0.074 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000100073
Gene: ENSMUSG00000028249
AA Change: I218V

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

noncoding transcript
Transcript: ENSMUST00000143704

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000149015

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

probably benign
Transcript: ENSMUST00000175769
AA Change: I219V

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000135777
Gene: ENSMUSG00000028249
AA Change: I219V

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156715

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 95.9%
20x: 90.9%

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: 98 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930486L24Rik	A	T	13: 61,001,414 (GRCm39)	H104Q	probably benign	Het
4933405L10Rik	A	G	8: 106,436,201 (GRCm39)	T158A	possibly damaging	Het
A1cf	T	C	19: 31,895,385 (GRCm39)	M156T	probably benign	Het
Abca15	A	G	7: 120,006,198 (GRCm39)	Y1620C	probably damaging	Het
Abca3	C	T	17: 24,593,274 (GRCm39)	R224C	probably damaging	Het
Ablim1	A	G	19: 57,062,285 (GRCm39)		probably null	Het
Acox2	A	T	14: 8,241,374 (GRCm38)	Y579*	probably null	Het
Adnp	A	T	2: 168,024,921 (GRCm39)	S791R	probably damaging	Het
Agbl1	A	G	7: 76,071,665 (GRCm39)	E329G	probably damaging	Het
Alx3	G	T	3: 107,512,109 (GRCm39)	S249I	possibly damaging	Het
Apob	A	G	12: 8,058,714 (GRCm39)	T2366A	probably benign	Het
Apool	C	T	X: 111,259,540 (GRCm39)	Q60*	probably null	Het
Arid4a	T	C	12: 71,091,853 (GRCm39)	V213A	probably benign	Het
Atp7a	A	G	X: 105,153,374 (GRCm39)	D1092G	probably benign	Het
Bpifa5	A	T	2: 154,007,892 (GRCm39)	E178V	probably damaging	Het
Car4	G	A	11: 84,854,193 (GRCm39)	E47K	probably benign	Het
Catsper1	T	C	19: 5,390,074 (GRCm39)		probably null	Het
Ccdc63	T	A	5: 122,259,118 (GRCm39)	Q260L	probably benign	Het
Ccdc83	A	T	7: 89,899,737 (GRCm39)	F45Y	probably damaging	Het
Cct8l1	G	A	5: 25,721,881 (GRCm39)	V199I	probably benign	Het
Cdc23	C	A	18: 34,784,742 (GRCm39)	V7L	unknown	Het
Ces5a	C	T	8: 94,261,296 (GRCm39)	V44M	probably damaging	Het
Cltc	A	G	11: 86,608,794 (GRCm39)	I741T	possibly damaging	Het
Cnst	C	A	1: 179,450,451 (GRCm39)	D638E	possibly damaging	Het
Col13a1	A	G	10: 61,709,797 (GRCm39)		silent	Het
Cyp2a22	A	T	7: 26,631,906 (GRCm39)	F450Y	probably benign	Het
Cyp2d10	C	T	15: 82,287,954 (GRCm39)	R383H	probably benign	Het
Cyp4a29	A	G	4: 115,104,860 (GRCm39)	T123A	probably benign	Het
Ddx20	A	G	3: 105,590,191 (GRCm39)		probably null	Het
Dnaja3	A	T	16: 4,514,289 (GRCm39)	T274S	probably damaging	Het
Dot1l	A	G	10: 80,620,480 (GRCm39)	D514G	possibly damaging	Het
Dysf	A	T	6: 84,114,254 (GRCm39)	K1226M	probably damaging	Het
Epha4	T	C	1: 77,421,639 (GRCm39)	Y281C	probably damaging	Het
Fbxo42	T	C	4: 140,926,256 (GRCm39)	W313R	probably damaging	Het
Fign	A	T	2: 63,810,037 (GRCm39)	L411*	probably null	Het
Flt1	C	A	5: 147,620,749 (GRCm39)	A132S	probably benign	Het
Fryl	G	A	5: 73,232,110 (GRCm39)	P1550L	probably damaging	Het
Gas2l3	CACTCGTCATACT	CACT	10: 89,266,820 (GRCm39)		probably benign	Het
Gprasp2	C	T	X: 134,743,346 (GRCm39)	T235I	possibly damaging	Het
Gtf2ird1	G	T	5: 134,419,787 (GRCm39)		probably null	Het
H2ab3	T	C	X: 119,222,543 (GRCm39)	T84A	probably damaging	Het
H2ac20	C	T	3: 96,128,099 (GRCm39)		probably benign	Het
Hal	A	T	10: 93,349,904 (GRCm39)	I555F	probably damaging	Het
Hdac6	A	G	X: 7,811,036 (GRCm39)	F104L	probably damaging	Homo
Hspg2	T	C	4: 137,267,541 (GRCm39)	S2050P	probably damaging	Het
Irgc	T	C	7: 24,132,196 (GRCm39)	D207G	probably benign	Het
Kif19a	G	A	11: 114,658,053 (GRCm39)	M37I	probably benign	Het
Kiss1r	C	A	10: 79,754,596 (GRCm39)	S30*	probably null	Het
Krtap1-4	C	G	11: 99,474,442 (GRCm39)		probably benign	Het
Lrrfip2	A	G	9: 111,028,872 (GRCm39)	E365G	probably damaging	Het
Ly75	A	G	2: 60,206,307 (GRCm39)	Y121H	probably damaging	Het
Man2a1	G	A	17: 64,966,074 (GRCm39)		probably null	Het
Mllt10	C	A	2: 18,114,685 (GRCm39)	H52N	possibly damaging	Het
Mrtfa	A	G	15: 80,906,627 (GRCm39)	V91A	probably damaging	Het
Myo1a	T	C	10: 127,543,288 (GRCm39)		probably null	Het
Myo3b	C	A	2: 69,925,593 (GRCm39)	T20K	possibly damaging	Het
Nipsnap2	A	T	5: 129,816,644 (GRCm39)	K62N	probably damaging	Het
Nr1i3	C	T	1: 171,044,382 (GRCm39)	T169I	probably benign	Het
Numbl	G	A	7: 26,980,415 (GRCm39)	D466N	probably damaging	Het
Oprm1	A	G	10: 6,782,550 (GRCm39)	S398G	probably benign	Het
Or14c46	A	G	7: 85,918,799 (GRCm39)	I66T	probably damaging	Het
Or51k1	T	A	7: 103,661,325 (GRCm39)	R195W	probably damaging	Het
Or6k2	A	T	1: 173,986,527 (GRCm39)	I63F	probably damaging	Het
Or8h10	A	T	2: 86,808,666 (GRCm39)	V158D	possibly damaging	Het
Pebp1	G	T	5: 117,421,475 (GRCm39)	D156E	probably benign	Het
Pik3c2g	T	A	6: 139,665,873 (GRCm39)	C65S	probably null	Het
Pilra	A	G	5: 137,833,674 (GRCm39)	F131L	probably damaging	Het
Pitrm1	T	C	13: 6,603,226 (GRCm39)	F91S	probably damaging	Het
Ppl	A	T	16: 4,906,742 (GRCm39)	S1184R	probably benign	Het
Prmt2	C	T	10: 76,058,390 (GRCm39)	V140I	probably damaging	Het
Psg29	T	A	7: 16,945,763 (GRCm39)	D444E	probably damaging	Het
Ptgs1	A	T	2: 36,141,272 (GRCm39)	N573I	probably damaging	Het
Pygb	C	T	2: 150,643,498 (GRCm39)	T95M	probably damaging	Het
Rassf9	A	G	10: 102,381,766 (GRCm39)	K383E	probably damaging	Het
Rfk	T	A	19: 17,375,963 (GRCm39)	F86I	possibly damaging	Het
Rims2	T	C	15: 39,325,986 (GRCm39)	F773L	probably benign	Het
Slc4a2	G	A	5: 24,643,760 (GRCm39)	S855N	probably benign	Het
Slc8a2	T	C	7: 15,884,508 (GRCm39)	L626P	possibly damaging	Het
Snrpd3	G	T	10: 75,355,227 (GRCm39)	C20F	possibly damaging	Het
Spen	A	T	4: 141,249,613 (GRCm39)	S58R	unknown	Het
St3gal2	T	C	8: 111,684,350 (GRCm39)	C3R	possibly damaging	Het
Stab2	A	T	10: 86,699,422 (GRCm39)	I481N	probably benign	Het
Stat5b	T	C	11: 100,699,361 (GRCm39)		probably null	Het
Tmco3	G	T	8: 13,342,860 (GRCm39)	E199*	probably null	Het
Tmem26	A	G	10: 68,611,178 (GRCm39)	T216A	probably damaging	Het
Ttn	A	G	2: 76,550,822 (GRCm39)		probably null	Het
Ttn	A	T	2: 76,602,709 (GRCm39)		probably null	Het
Ttn	C	T	2: 76,576,746 (GRCm39)	V24716I	probably damaging	Het
Uba5	T	C	9: 103,931,626 (GRCm39)	E202G	probably damaging	Het
Ufl1	A	G	4: 25,254,780 (GRCm39)	Y559H	probably benign	Het
Utrn	A	T	10: 12,259,948 (GRCm39)		probably null	Het
Vmn2r111	C	A	17: 22,767,022 (GRCm39)	C825F	probably damaging	Het
Vmn2r113	T	A	17: 23,177,329 (GRCm39)	C704*	probably null	Het
Vmn2r56	A	G	7: 12,427,983 (GRCm39)	I761T	probably benign	Het
Vmn2r98	C	T	17: 19,286,306 (GRCm39)	T268I	probably benign	Het
Zfp263	A	G	16: 3,564,704 (GRCm39)	R240G	possibly damaging	Het
Zfp473	T	A	7: 44,381,943 (GRCm39)	I797F	probably damaging	Het
Zfp68	A	T	5: 138,604,579 (GRCm39)	D543E	probably benign	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
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
R7483:Sdcbp	UTSW	4	6,393,089 (GRCm39)	missense	possibly damaging	0.95
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'- AGTTAGAAACACCACTTTCTGTATC -3'
(R):5'- CTAGCTCAAGGGATTCCAGG -3'

Sequencing Primer
(F):5'- TCAAAATATCCCATGTGGCAGAG -3'
(R):5'- CAGATGTGGTGATCAGTG -3'

Posted On

2016-06-06