Mutagenetix > Incidental Mutation

Incidental Mutation 'R2006:Sdcbp'

225512

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

040015-MU

Accession Numbers

Essential gene?

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

Stock #

R2006 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

6365654-6396122 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 6386536 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Leucine at position 137 (I137L)

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: I137L

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

SMART Domains

Protein: ENSMUSP00000029912
Gene: ENSMUSG00000028249
AA Change: I137L

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: I136L

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000100073
Gene: ENSMUSG00000028249
AA Change: I136L

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 benign
Transcript: ENSMUST00000108374
AA Change: I137L

PolyPhen 2 Score 0.233 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000104011
Gene: ENSMUSG00000028249
AA Change: I137L

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
AA Change: I136L

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000119838
Gene: ENSMUSG00000028249
AA Change: I136L

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

Predicted Effect

probably benign
Transcript: ENSMUST00000175769
AA Change: I137L

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000135777
Gene: ENSMUSG00000028249
AA Change: I137L

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

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.2%

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: 97 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca5	A	T	11: 110,204,275 (GRCm39)	F333L	probably benign	Het
Abcc2	T	A	19: 43,793,500 (GRCm39)	F384Y	probably damaging	Het
Acr	C	T	15: 89,458,404 (GRCm39)	P362S	probably benign	Het
Acss3	T	C	10: 106,798,871 (GRCm39)	D484G	possibly damaging	Het
Actrt1	A	G	X: 45,418,593 (GRCm39)	T203A	probably benign	Het
Agtpbp1	A	T	13: 59,648,135 (GRCm39)	C562S	probably benign	Het
Ahnak	A	G	19: 8,984,439 (GRCm39)	K1908E	probably damaging	Het
Amph	G	A	13: 19,326,198 (GRCm39)	V643M	probably damaging	Het
Apaf1	A	T	10: 90,897,634 (GRCm39)	I283N	probably damaging	Het
Bbx	G	A	16: 50,044,758 (GRCm39)	T493M	possibly damaging	Het
Best2	C	T	8: 85,739,818 (GRCm39)		probably null	Het
C4bp	C	A	1: 130,575,769 (GRCm39)	E75*	probably null	Het
Calr3	A	T	8: 73,188,695 (GRCm39)	V144D	probably damaging	Het
Capn1	C	T	19: 6,041,613 (GRCm39)	G632D	probably damaging	Het
Catsper2	C	A	2: 121,236,838 (GRCm39)	E270*	probably null	Het
Ccdc110	A	T	8: 46,396,349 (GRCm39)	I747F	probably damaging	Het
Ccdc15	T	A	9: 37,226,768 (GRCm39)	D389V	possibly damaging	Het
Cd226	A	G	18: 89,265,435 (GRCm39)	I125V	probably benign	Het
Crb2	A	T	2: 37,673,446 (GRCm39)	D114V	probably damaging	Het
Crebbp	TTGCTGCTGCTGCTGCTG	TTGCTGCTGCTGCTG	16: 3,902,617 (GRCm39)		probably benign	Het
Crebrf	T	C	17: 26,961,857 (GRCm39)	V318A	possibly damaging	Het
Dab1	T	C	4: 104,462,522 (GRCm39)	I32T	probably damaging	Het
Daw1	T	C	1: 83,169,066 (GRCm39)	V181A	probably damaging	Het
Dlg2	G	A	7: 91,614,825 (GRCm39)	E255K	possibly damaging	Het
Dnah10	T	A	5: 124,906,651 (GRCm39)	D4170E	possibly damaging	Het
Dnah12	A	G	14: 26,536,416 (GRCm39)	T2111A	possibly damaging	Het
Dock10	T	C	1: 80,527,506 (GRCm39)	Y1081C	possibly damaging	Het
Dscam	T	C	16: 96,621,112 (GRCm39)	Y532C	probably damaging	Het
Fam83c	T	C	2: 155,672,223 (GRCm39)	D404G	probably benign	Het
Fam83g	A	G	11: 61,593,801 (GRCm39)	N445S	possibly damaging	Het
Ghr	C	T	15: 3,357,464 (GRCm39)	C268Y	probably damaging	Het
Gm8444	T	C	15: 81,727,775 (GRCm39)		probably benign	Het
Gp6	T	A	7: 4,387,988 (GRCm39)	K160N	probably benign	Het
Grm3	T	C	5: 9,639,793 (GRCm39)	Y84C	possibly damaging	Het
Gtf3c2	C	A	5: 31,325,440 (GRCm39)	G450C	probably damaging	Het
Icosl	A	T	10: 77,907,787 (GRCm39)	M116L	possibly damaging	Het
Il31ra	T	G	13: 112,666,890 (GRCm39)	Y396S	probably damaging	Het
Insig1	A	G	5: 28,276,464 (GRCm39)	N10S	probably benign	Het
Kcnh2	C	A	5: 24,531,568 (GRCm39)	G448C	probably damaging	Het
L1td1	C	T	4: 98,621,726 (GRCm39)	S96L	possibly damaging	Het
Mapre3	A	T	5: 31,019,168 (GRCm39)	N4I	probably damaging	Het
Mblac2	T	A	13: 81,859,860 (GRCm39)	D70E	probably benign	Het
Mki67	T	A	7: 135,300,238 (GRCm39)	K1599*	probably null	Het
Mpg	A	G	11: 32,181,840 (GRCm39)	I283V	probably benign	Het
Mrtfb	G	T	16: 13,199,440 (GRCm39)	E98*	probably null	Het
Mybpc1	C	A	10: 88,381,921 (GRCm39)	A576S	probably damaging	Het
Myo1h	T	G	5: 114,499,140 (GRCm39)	V129G	probably damaging	Het
Nars1	A	T	18: 64,638,099 (GRCm39)	V285E	probably damaging	Het
Nbas	T	A	12: 13,464,742 (GRCm39)		probably null	Het
Neb	T	C	2: 52,089,456 (GRCm39)	D5172G	probably null	Het
Npbwr1	T	A	1: 5,986,570 (GRCm39)	S315C	probably damaging	Het
Nyap1	T	C	5: 137,733,953 (GRCm39)	H360R	possibly damaging	Het
Nyx	A	G	X: 13,352,974 (GRCm39)	E276G	probably damaging	Het
Or10ag59	T	A	2: 87,405,536 (GRCm39)	M36K	probably benign	Het
Or1e1	G	T	11: 73,245,518 (GRCm39)	C313F	probably benign	Het
Or2l13b	A	G	16: 19,349,455 (GRCm39)	Y72H	probably benign	Het
Or2w6	T	C	13: 21,842,642 (GRCm39)	T284A	possibly damaging	Het
Or4c1	A	G	2: 89,133,160 (GRCm39)	Y259H	possibly damaging	Het
Or4c118	A	T	2: 88,975,241 (GRCm39)	V42E	probably benign	Het
Or5v1b	C	T	17: 37,841,597 (GRCm39)	S243F	probably damaging	Het
Or7e174	A	T	9: 20,012,165 (GRCm39)	M37L	probably benign	Het
Or7g16	G	A	9: 18,726,801 (GRCm39)	S263L	probably benign	Het
Or8g23	T	A	9: 38,971,729 (GRCm39)	T78S	probably damaging	Het
Paf1	C	A	7: 28,095,193 (GRCm39)		probably null	Het
Pcsk5	T	C	19: 17,455,280 (GRCm39)	D1050G	probably benign	Het
Pgap1	A	G	1: 54,590,220 (GRCm39)	S73P	possibly damaging	Het
Phtf1	G	A	3: 103,911,799 (GRCm39)		probably null	Het
Pik3c2b	G	T	1: 132,994,282 (GRCm39)	R82L	probably damaging	Het
Pik3ca	T	C	3: 32,504,206 (GRCm39)	L632P	probably damaging	Het
Plau	G	T	14: 20,888,760 (GRCm39)		probably null	Het
Pld4	A	T	12: 112,734,923 (GRCm39)	Q460L	possibly damaging	Het
Prdm2	T	A	4: 142,858,447 (GRCm39)	Q1614H	possibly damaging	Het
Ptprq	C	T	10: 107,502,407 (GRCm39)	G837D	probably damaging	Het
Rad9b	A	G	5: 122,477,842 (GRCm39)	V178A	possibly damaging	Het
Rfc1	G	T	5: 65,468,397 (GRCm39)	Y105*	probably null	Het
Sardh	G	A	2: 27,118,351 (GRCm39)	R460C	probably damaging	Het
Scn5a	C	A	9: 119,365,546 (GRCm39)	R367L	probably damaging	Het
Shmt2	A	G	10: 127,355,029 (GRCm39)	V273A	probably benign	Het
Slc5a9	G	T	4: 111,737,423 (GRCm39)	P612H	probably benign	Het
Slitrk4	TTGT	TT	X: 63,314,294 (GRCm39)		probably null	Het
Slitrk4	TG	T	X: 63,314,295 (GRCm39)		probably null	Het
Spata1	A	T	3: 146,199,438 (GRCm39)	S9T	probably benign	Het
Syn3	T	C	10: 85,909,097 (GRCm39)	T328A	probably benign	Het
Tdrd6	A	G	17: 43,939,546 (GRCm39)	F501L	probably damaging	Het
Tekt5	T	C	16: 10,213,070 (GRCm39)	I72V	probably benign	Het
Ticrr	T	C	7: 79,343,821 (GRCm39)	S1229P	possibly damaging	Het
Tlr6	T	C	5: 65,110,748 (GRCm39)	S720G	probably damaging	Het
Tmem156	T	A	5: 65,237,294 (GRCm39)	D87V	probably damaging	Het
Togaram1	T	A	12: 65,065,914 (GRCm39)	D1639E	probably damaging	Het
Ucn2	A	G	9: 108,815,430 (GRCm39)	K64R	probably benign	Het
Vmn2r57	T	A	7: 41,098,001 (GRCm39)	Y22F	probably benign	Het
Vwa1	T	C	4: 155,855,307 (GRCm39)	T269A	probably benign	Het
Washc5	A	G	15: 59,213,004 (GRCm39)	L892P	possibly damaging	Het
Wdr20	T	C	12: 110,760,002 (GRCm39)	V296A	probably damaging	Het
Xxylt1	A	T	16: 30,869,586 (GRCm39)	H171Q	probably damaging	Het
Yju2	C	T	17: 56,271,543 (GRCm39)	Q155*	probably null	Het
Zfp275	A	G	X: 72,396,841 (GRCm39)	T118A	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
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'- CCCCAATTTCATCGGTTAAGAGG -3'
(R):5'- ACGGATCGTCATGGTGATC -3'

Sequencing Primer
(F):5'- GGAATTGTTACCCCAAAGTATCAC -3'
(R):5'- ACGGATCGTCATGGTGATCTTCTC -3'

Posted On

2014-08-25