Mutagenetix > Incidental Mutation

Incidental Mutation 'R0158:Sdcbp'

22958

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

038438-MU

Accession Numbers

Essential gene?

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

Stock #

R0158 (G1)

Quality Score

201

Status

Validated

Chromosome

Chromosomal Location

6365654-6396122 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 6379042 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 43 (D43G)

Ref Sequence

ENSEMBL: ENSMUSP00000104011 (fasta)

Gene Model

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

AlphaFold

O08992

Predicted Effect

probably benign
Transcript: ENSMUST00000029912
AA Change: D43G

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000029912
Gene: ENSMUSG00000028249
AA Change: D43G

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: D43G

PolyPhen 2 Score 0.267 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000100073
Gene: ENSMUSG00000028249
AA Change: D43G

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

possibly damaging
Transcript: ENSMUST00000108374
AA Change: D43G

PolyPhen 2 Score 0.811 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000104011
Gene: ENSMUSG00000028249
AA Change: D43G

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

Predicted Effect

probably benign
Transcript: ENSMUST00000140830
AA Change: D43G

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

SMART Domains

Protein: ENSMUSP00000122411
Gene: ENSMUSG00000028249
AA Change: D43G

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

Predicted Effect

probably benign
Transcript: ENSMUST00000153861
AA Change: D43G

PolyPhen 2 Score 0.267 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000119838
Gene: ENSMUSG00000028249
AA Change: D43G

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155247

Predicted Effect

probably benign
Transcript: ENSMUST00000175769
AA Change: D43G

PolyPhen 2 Score 0.441 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000135777
Gene: ENSMUSG00000028249
AA Change: D43G

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

0.0755

Coding Region Coverage

1x: 98.9%
3x: 97.9%
10x: 95.3%
20x: 89.1%

Validation Efficiency

93% (79/85)

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcf3	C	T	16: 20,371,316 (GRCm39)	R437C	probably damaging	Het
Abhd3	A	G	18: 10,647,840 (GRCm39)	Y315H	possibly damaging	Het
Adam19	C	T	11: 46,033,861 (GRCm39)	P891L	probably damaging	Het
Ampd1	T	A	3: 102,999,046 (GRCm39)	Y400*	probably null	Het
Ap1g1	T	C	8: 110,582,267 (GRCm39)	S724P	probably benign	Het
Bst2	T	A	8: 71,989,861 (GRCm39)	T71S	possibly damaging	Het
C3	A	G	17: 57,531,851 (GRCm39)		probably null	Het
Cacna2d1	C	A	5: 16,566,815 (GRCm39)		probably benign	Het
Cacna2d4	C	T	6: 119,213,709 (GRCm39)	H43Y	possibly damaging	Het
Ccdc71	T	G	9: 108,341,336 (GRCm39)	V383G	probably benign	Het
Cd109	A	T	9: 78,596,214 (GRCm39)	Q849L	possibly damaging	Het
Cdkn2a	A	T	4: 89,195,004 (GRCm39)	H115Q	possibly damaging	Het
Ces1e	T	C	8: 93,946,057 (GRCm39)	E161G	probably benign	Het
Cggbp1	C	T	16: 64,676,201 (GRCm39)	S89L	possibly damaging	Het
Crocc	A	T	4: 140,769,553 (GRCm39)		probably benign	Het
Cspg4b	T	A	13: 113,505,687 (GRCm39)	L2272*	probably null	Het
Eef1akmt3	G	A	10: 126,869,142 (GRCm39)	Q111*	probably null	Het
Exoc7	T	C	11: 116,186,118 (GRCm39)	N361S	probably benign	Het
Fat2	G	T	11: 55,187,011 (GRCm39)	S1278R	probably benign	Het
Fbxo42	A	G	4: 140,927,640 (GRCm39)	N640S	probably benign	Het
Fbxw25	A	G	9: 109,483,720 (GRCm39)	V164A	possibly damaging	Het
Fcgbpl1	A	G	7: 27,854,917 (GRCm39)	I1848V	probably damaging	Het
Foxs1	T	C	2: 152,774,330 (GRCm39)	E241G	probably damaging	Het
Fras1	A	T	5: 96,924,493 (GRCm39)	I3645F	possibly damaging	Het
Gm14496	T	A	2: 181,639,206 (GRCm39)	V432E	probably benign	Het
H3c2	T	A	13: 23,936,693 (GRCm39)	C111S	probably damaging	Het
Herc1	T	A	9: 66,403,203 (GRCm39)	L4374*	probably null	Het
Ift122	T	C	6: 115,901,445 (GRCm39)		probably benign	Het
Itgav	C	A	2: 83,622,381 (GRCm39)	N654K	probably benign	Het
Itih5	T	C	2: 10,239,803 (GRCm39)		probably benign	Het
Jak2	C	A	19: 29,289,157 (GRCm39)	T1103K	probably benign	Het
Kcnc4	C	A	3: 107,365,920 (GRCm39)	C96F	probably benign	Het
Med13l	C	A	5: 118,880,514 (GRCm39)	S1202Y	unknown	Het
Mefv	T	C	16: 3,533,320 (GRCm39)	E317G	possibly damaging	Het
Ncoa2	T	C	1: 13,222,608 (GRCm39)	T1226A	probably benign	Het
Nktr	C	T	9: 121,579,757 (GRCm39)		probably benign	Het
Nudt5	G	A	2: 5,867,114 (GRCm39)	V61M	probably damaging	Het
Or51a39	C	T	7: 102,363,162 (GRCm39)	A153T	probably benign	Het
Pakap	A	G	4: 57,709,649 (GRCm39)	D198G	possibly damaging	Het
Pcdhb2	A	C	18: 37,430,283 (GRCm39)	Y752S	probably damaging	Het
Pcnx4	A	G	12: 72,603,076 (GRCm39)	D446G	probably benign	Het
Pnp2	G	A	14: 51,201,761 (GRCm39)	R249H	probably damaging	Het
Rgs3	A	T	4: 62,542,121 (GRCm39)	I32F	probably damaging	Het
Rnf139	A	G	15: 58,770,727 (GRCm39)	T251A	probably benign	Het
Rnf41	A	G	10: 128,274,104 (GRCm39)	E252G	probably damaging	Het
Rxfp2	T	A	5: 149,975,093 (GRCm39)	F220Y	probably benign	Het
Serpina3f	A	G	12: 104,183,267 (GRCm39)	D43G	probably damaging	Het
Sftpc	T	C	14: 70,758,887 (GRCm39)	K154R	probably null	Het
Simc1	A	G	13: 54,672,530 (GRCm39)	T293A	probably benign	Het
Skint6	A	T	4: 113,042,011 (GRCm39)		probably benign	Het
Slc6a15	T	C	10: 103,225,208 (GRCm39)		probably benign	Het
Spata31e2	T	G	1: 26,723,032 (GRCm39)	H716P	probably damaging	Het
Ston2	A	T	12: 91,707,376 (GRCm39)	I78N	probably damaging	Het
Taok3	T	C	5: 117,355,307 (GRCm39)		probably null	Het
Tent4b	G	A	8: 88,977,371 (GRCm39)	G391D	probably damaging	Het
Tiam1	C	T	16: 89,589,889 (GRCm39)		probably benign	Het
Tnfsf15	T	C	4: 63,648,229 (GRCm39)	H137R	possibly damaging	Het
Tpte	G	A	8: 22,817,755 (GRCm39)	R247H	possibly damaging	Het
Trim2	T	C	3: 84,117,476 (GRCm39)		probably benign	Het
Ulk1	A	T	5: 110,936,810 (GRCm39)		probably benign	Het
Utp4	T	G	8: 107,640,018 (GRCm39)	H442Q	probably null	Het
Vmn1r193	T	A	13: 22,403,798 (GRCm39)	I65F	probably damaging	Het
Vps54	A	T	11: 21,256,962 (GRCm39)	Q690L	probably damaging	Het
Ybx2	T	C	11: 69,831,145 (GRCm39)		probably benign	Het
Zbtb38	C	T	9: 96,568,993 (GRCm39)	G697D	possibly damaging	Het
Zfp202	C	T	9: 40,120,212 (GRCm39)	Q218*	probably null	Het
Zfp820	G	A	17: 22,038,800 (GRCm39)	T176I	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
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
R9093:Sdcbp	UTSW	4	6,386,709 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- GCAGGCACACTGTTAGGCACT -3'
(R):5'- TGCCCTAAGACTCACCTTCATACTCAAA -3'

Sequencing Primer
(F):5'- CCTTTGGGTGAAAATGATTTCTGAAC -3'
(R):5'- ATTTCAGGGGAGAAGAAGGCCT -3'

Posted On

2013-04-16