Mutagenetix > Incidental Mutation

Incidental Mutation 'R9093:Sdcbp'

691121

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

Accession Numbers

Essential gene?

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

Stock #

R9093 (G1)

Quality Score

225.009

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 T at 6386709 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000029912 (fasta)

Gene Model

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

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: ENSMUST00000140830

SMART Domains

Protein: ENSMUSP00000122411
Gene: ENSMUSG00000028249

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

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

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

Validation Efficiency

97% (76/78)

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: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb11	A	T	2: 69,069,513 (GRCm39)	V1294E	probably damaging	Het
Ada	C	T	2: 163,577,308 (GRCm39)	G60D	probably benign	Het
Aff3	G	T	1: 38,291,738 (GRCm39)	R390S	possibly damaging	Het
Aldh3b3	T	A	19: 4,013,959 (GRCm39)	N53K	possibly damaging	Het
Ankrd36	G	A	11: 5,589,132 (GRCm39)	M410I	probably benign	Het
Ap2b1	T	A	11: 83,215,395 (GRCm39)	I113N	probably damaging	Het
Art5	G	T	7: 101,747,396 (GRCm39)	H128N	probably benign	Het
Calhm2	A	C	19: 47,121,599 (GRCm39)	L190R	probably benign	Het
Catsperg1	G	C	7: 28,884,152 (GRCm39)	T987R	probably damaging	Het
Cdh18	A	T	15: 23,474,064 (GRCm39)	I645F	probably damaging	Het
Cenpe	C	T	3: 134,945,641 (GRCm39)	Q1052*	probably null	Het
Cfap221	G	T	1: 119,863,856 (GRCm39)	Q563K	probably damaging	Het
Cfap54	T	A	10: 92,651,770 (GRCm39)	E3093D	probably benign	Het
Chd4	A	G	6: 125,090,974 (GRCm39)	M1186V	probably benign	Het
Chst15	A	T	7: 131,870,646 (GRCm39)		probably null	Het
Clca3a2	T	C	3: 144,781,481 (GRCm39)	T688A	probably benign	Het
Cmtm1	TCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGG	TCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGGCTGGCTGGTGTCCCGGGTACTGAAGGTCCCTGG	8: 105,036,334 (GRCm39)		probably null	Het
Cul1	T	A	6: 47,495,173 (GRCm39)	N518K	probably damaging	Het
E230025N22Rik	G	T	18: 36,821,952 (GRCm39)	L247I	possibly damaging	Het
Eno4	A	T	19: 58,941,600 (GRCm39)	K174*	probably null	Het
Enpp3	G	A	10: 24,671,702 (GRCm39)	P431S	probably benign	Het
Fbh1	T	A	2: 11,764,801 (GRCm39)	Q444H	probably damaging	Het
Fbxo31	G	A	8: 122,281,136 (GRCm39)	R337C	probably damaging	Het
Fbxw14	A	G	9: 109,105,250 (GRCm39)	I305T	probably benign	Het
Fhip1b	T	A	7: 105,034,599 (GRCm39)	T408S	probably damaging	Het
Gas2	T	A	7: 51,602,969 (GRCm39)	C216S	probably damaging	Het
Gjb3	GCCAGATGCGCCCA	GCCAGATGCGCCCAGATGCGCCCA	4: 127,220,458 (GRCm39)		probably null	Het
Glp2r	T	A	11: 67,621,459 (GRCm39)	R344*	probably null	Het
Gm17430	A	G	18: 9,726,640 (GRCm39)	Y11H	probably damaging	Het
Gyg1	T	A	3: 20,176,901 (GRCm39)	D363V	probably damaging	Het
H2bc18	G	A	3: 96,177,290 (GRCm39)	A75T	probably benign	Het
Hectd4	A	G	5: 121,411,677 (GRCm39)	N451S	probably benign	Het
Hif1a	T	C	12: 73,979,111 (GRCm39)	Y212H	probably benign	Het
Hoxd11	A	T	2: 74,514,482 (GRCm39)	*337C	probably null	Het
Kif24	A	G	4: 41,428,691 (GRCm39)	F90L	probably benign	Het
Klhl20	A	T	1: 160,923,231 (GRCm39)	C497*	probably null	Het
Loxl1	C	A	9: 58,219,224 (GRCm39)	A316S	probably benign	Het
Lrig3	C	T	10: 125,845,950 (GRCm39)	P793L	possibly damaging	Het
Macc1	A	G	12: 119,410,561 (GRCm39)	D443G	probably benign	Het
Maip1	A	T	1: 57,446,311 (GRCm39)	Y127F	possibly damaging	Het
Mrm2	A	T	5: 140,314,427 (GRCm39)	F136Y	probably benign	Het
Nasp	G	T	4: 116,468,017 (GRCm39)	L323I	probably benign	Het
Ndufb8	A	T	19: 44,538,823 (GRCm39)	L166Q	probably damaging	Het
Nid2	C	T	14: 19,858,009 (GRCm39)	T1274I		Het
Nup210	T	A	6: 91,066,872 (GRCm39)	T160S	probably benign	Het
Nutm2	A	G	13: 50,628,964 (GRCm39)	K676R	probably damaging	Het
Odad1	G	A	7: 45,596,965 (GRCm39)	V431I	possibly damaging	Het
Or10a3n	T	C	7: 108,493,609 (GRCm39)	R7G	probably benign	Het
Or2a20	A	G	6: 43,194,500 (GRCm39)	T218A	probably benign	Het
Or56b1b	A	T	7: 108,164,454 (GRCm39)	C183S	probably damaging	Het
Or5ak20	T	A	2: 85,183,852 (GRCm39)	R139S	probably benign	Het
Or7g33	A	G	9: 19,448,914 (GRCm39)	V104A	probably benign	Het
Or8b9	A	T	9: 37,766,294 (GRCm39)	Y60F	probably damaging	Het
Or9m1	A	T	2: 87,733,480 (GRCm39)	I180N	probably benign	Het
Pcdhga12	C	A	18: 37,899,931 (GRCm39)	N254K	possibly damaging	Het
Pm20d1	G	T	1: 131,743,753 (GRCm39)	V473F	probably benign	Het
Pou2af2	G	A	9: 51,201,516 (GRCm39)	P180L	possibly damaging	Het
Rab11fip1	A	G	8: 27,633,355 (GRCm39)	V596A	probably damaging	Het
Rapgef6	C	T	11: 54,487,912 (GRCm39)	Q13*	probably null	Het
Rasef	T	C	4: 73,698,583 (GRCm39)	D26G	probably benign	Het
Rbfox2	A	T	15: 77,190,658 (GRCm39)	V29E	probably benign	Het
Recql4	G	A	15: 76,589,685 (GRCm39)	P787S	unknown	Het
Rnf19a	A	C	15: 36,253,450 (GRCm39)		probably benign	Het
Rnf214	A	G	9: 45,811,054 (GRCm39)	I203T	probably damaging	Het
Rnmt	A	C	18: 68,451,146 (GRCm39)	E396D	probably benign	Het
Scn4a	G	A	11: 106,210,638 (GRCm39)	S1793L	probably benign	Het
Slfn3	A	G	11: 83,103,948 (GRCm39)	N273S	probably damaging	Het
Slk	A	G	19: 47,603,883 (GRCm39)	D209G		Het
Tent5b	A	G	4: 133,214,352 (GRCm39)	T408A	probably damaging	Het
Tmem135	T	A	7: 88,797,204 (GRCm39)	M351L	probably benign	Het
Tmem64	A	G	4: 15,266,391 (GRCm39)	H147R	probably benign	Het
Tnfsf4	T	C	1: 161,244,629 (GRCm39)	L106P	probably damaging	Het
Tonsl	A	T	15: 76,515,270 (GRCm39)	C1039S	probably damaging	Het
Ube4a	A	T	9: 44,864,462 (GRCm39)	F44I	possibly damaging	Het
Vmn2r40	A	G	7: 8,911,172 (GRCm39)	L707P		Het
Vmn2r87	G	A	10: 130,308,165 (GRCm39)	T691I	probably benign	Het
Wbp11	A	T	6: 136,803,044 (GRCm39)	S7T	possibly damaging	Het
Zfp386	C	A	12: 116,023,878 (GRCm39)	S532*	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
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
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

Predicted Primers

PCR Primer
(F):5'- TTGTTCAACTCGTCCAGGC -3'
(R):5'- AGAAACATTATGTGGACTCAAATGG -3'

Sequencing Primer
(F):5'- GTCCAGGCTAATTCCCCAG -3'
(R):5'- GGATGGGCACACACTCAGATTTTTAC -3'

Posted On

2021-12-30