Mutagenetix > Incidental Mutation

Incidental Mutation 'R1115:Sdcbp'

97139

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

039188-MU

Accession Numbers

Essential gene?

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

Stock #

R1115 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

6365654-6396122 bp(+) (GRCm39)

Type of Mutation

critical splice donor site (1 bp from exon)

DNA Base Change (assembly)

G to A at 6377143 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000135777 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029912] [ENSMUST00000103008] [ENSMUST00000108374] [ENSMUST00000140830] [ENSMUST00000140830] [ENSMUST00000153861] [ENSMUST00000153861] [ENSMUST00000175769]

AlphaFold

O08992

Predicted Effect

probably null
Transcript: ENSMUST00000029912

SMART Domains

Protein: ENSMUSP00000029912
Gene: ENSMUSG00000028249

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

Predicted Effect

probably null
Transcript: ENSMUST00000103008

SMART Domains

Protein: ENSMUSP00000100073
Gene: ENSMUSG00000028249

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000108371

Predicted Effect

probably null
Transcript: ENSMUST00000108374

SMART Domains

Protein: ENSMUSP00000104011
Gene: ENSMUSG00000028249

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

Predicted Effect

probably null
Transcript: ENSMUST00000140830

SMART Domains

Protein: ENSMUSP00000122411
Gene: ENSMUSG00000028249

Domain	Start	End	E-Value	Type
Blast:PDZ	56	91	1e-10	BLAST

Predicted Effect

probably null
Transcript: ENSMUST00000140830

SMART Domains

Protein: ENSMUSP00000122411
Gene: ENSMUSG00000028249

Domain	Start	End	E-Value	Type
Blast:PDZ	56	91	1e-10	BLAST

Predicted Effect

probably null
Transcript: ENSMUST00000153861

SMART Domains

Protein: ENSMUSP00000119838
Gene: ENSMUSG00000028249

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

Predicted Effect

probably null
Transcript: ENSMUST00000153861

SMART Domains

Protein: ENSMUSP00000119838
Gene: ENSMUSG00000028249

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155247

Predicted Effect

probably null
Transcript: ENSMUST00000175769

SMART Domains

Protein: ENSMUSP00000135777
Gene: ENSMUSG00000028249

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: ENSMUST00000193139

Meta Mutation Damage Score

0.9653

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 95.9%
20x: 91.8%

Validation Efficiency

100% (34/34)

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: 34 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acly	C	A	11: 100,370,081 (GRCm39)	V994F	probably damaging	Het
Arfgap3	T	C	15: 83,214,741 (GRCm39)	T182A	probably benign	Het
Bcl2l14	T	C	6: 134,409,102 (GRCm39)		probably benign	Het
Cabin1	T	C	10: 75,553,511 (GRCm39)	M1183V	possibly damaging	Het
Ccr7	A	T	11: 99,036,103 (GRCm39)	I273K	possibly damaging	Het
Cd40	A	G	2: 164,912,681 (GRCm39)	M211V	possibly damaging	Het
Coro2b	T	G	9: 62,338,609 (GRCm39)	E208A	probably damaging	Het
Dennd5a	A	C	7: 109,517,968 (GRCm39)	M556R	probably damaging	Het
Efcab2	A	T	1: 178,265,062 (GRCm39)		probably benign	Het
Fastkd2	T	C	1: 63,787,114 (GRCm39)		probably benign	Het
Fbxw8	A	C	5: 118,215,636 (GRCm39)		probably benign	Het
Fhip1a	T	C	3: 85,629,802 (GRCm39)	E263G	probably benign	Het
Frem1	T	C	4: 82,939,007 (GRCm39)	D25G	probably benign	Het
Gtf3c3	C	T	1: 54,456,937 (GRCm39)	A488T	probably damaging	Het
Ift52	A	G	2: 162,871,702 (GRCm39)	K178R	probably benign	Het
Kit	T	C	5: 75,810,192 (GRCm39)		probably benign	Het
Map1a	T	C	2: 121,137,859 (GRCm39)		probably null	Het
Mxra7	G	T	11: 116,701,696 (GRCm39)		probably benign	Het
Myt1	C	A	2: 181,453,024 (GRCm39)	S7*	probably null	Het
Nphs1	C	T	7: 30,180,803 (GRCm39)		probably benign	Het
Or10h28	C	T	17: 33,487,940 (GRCm39)	R81*	probably null	Het
Or1l8	C	A	2: 36,817,514 (GRCm39)	G204V	possibly damaging	Het
Osgin2	A	T	4: 15,998,085 (GRCm39)	D512E	possibly damaging	Het
Pde4b	T	A	4: 102,399,352 (GRCm39)		probably benign	Het
Rasef	G	T	4: 73,666,841 (GRCm39)	T146K	possibly damaging	Het
Ren1	T	A	1: 133,284,256 (GRCm39)	V207D	probably damaging	Het
S100a8	A	G	3: 90,577,180 (GRCm39)	D59G	probably damaging	Het
Sdk2	C	T	11: 113,729,472 (GRCm39)		silent	Het
Slamf7	A	T	1: 171,466,751 (GRCm39)	D151E	probably benign	Het
Slco1b2	A	G	6: 141,628,980 (GRCm39)	M561V	probably benign	Het
Sned1	G	A	1: 93,209,376 (GRCm39)	V830M	possibly damaging	Het
Stard9	T	C	2: 120,523,331 (GRCm39)	I662T	probably benign	Het
Vwf	T	A	6: 125,632,028 (GRCm39)	V20D	unknown	Het
Znhit6	G	T	3: 145,300,440 (GRCm39)		probably null	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
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
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'- TGTGGGAACAGAGAGACAGTTTGGTA -3'
(R):5'- CCAATGGGAAGGAagggaggga -3'

Sequencing Primer
(F):5'- CAGAGAGACAGTTTGGTAACAGC -3'
(R):5'- aagggagggagggaggg -3'

Posted On

2014-01-05