Mutagenetix > Incidental Mutations

Incidental Mutation 'R4700:Sdc1'

355954

Institutional Source

Beutler Lab

Gene Symbol

Sdc1

Ensembl Gene

ENSMUSG00000020592

Gene Name

syndecan 1

Synonyms

Synd1, syn-1, CD138, Synd

MMRRC Submission

041948-MU

Accession Numbers

Is this an essential gene?

Possibly non essential (E-score: 0.260) question?

Stock #

R4700 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

8771323-8793715 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 8790541 bp

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 106 (E106G)

Ref Sequence

ENSEMBL: ENSMUSP00000123896 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020911] [ENSMUST00000161883] [ENSMUST00000171158]

Predicted Effect

probably benign
Transcript: ENSMUST00000020911
AA Change: E102G

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000020911
Gene: ENSMUSG00000020592
AA Change: E102G

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
low complexity region	33	50	N/A	INTRINSIC
low complexity region	71	86	N/A	INTRINSIC
low complexity region	137	152	N/A	INTRINSIC
low complexity region	253	266	N/A	INTRINSIC
4.1m	276	294	5.47e-6	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000159821

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160348

Predicted Effect

possibly damaging
Transcript: ENSMUST00000161883
AA Change: E106G

PolyPhen 2 Score 0.816 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000123896
Gene: ENSMUSG00000020592
AA Change: E106G

Domain	Start	End	E-Value	Type
low complexity region	37	54	N/A	INTRINSIC
low complexity region	75	90	N/A	INTRINSIC
low complexity region	141	156	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000171158
AA Change: E102G

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000131491
Gene: ENSMUSG00000020592
AA Change: E102G

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
low complexity region	33	50	N/A	INTRINSIC
low complexity region	71	86	N/A	INTRINSIC
low complexity region	137	152	N/A	INTRINSIC
low complexity region	253	266	N/A	INTRINSIC
4.1m	276	294	5.47e-6	SMART

Meta Mutation Damage Score

0.1241

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.8%
20x: 94.0%

Validation Efficiency

97% (127/131)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan and is a member of the syndecan proteoglycan family. The syndecans mediate cell binding, cell signaling, and cytoskeletal organization and syndecan receptors are required for internalization of the HIV-1 tat protein. The syndecan-1 protein functions as an integral membrane protein and participates in cell proliferation, cell migration and cell-matrix interactions via its receptor for extracellular matrix proteins. Altered syndecan-1 expression has been detected in several different tumor types. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode the same protein. [provided by RefSeq, Jul 2008]
PHENOTYPE: Targeted mutant mice are overtly normal but resist mammary tumor development in response to Wnt1, and show delayed cutaneous and corneal wound healing, defective leukocyte adhesion to endothelia, increased angiogenesis, as well as reduced susceptibility to P. aeruginosa lung infection. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 112 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A530084C06Rik	A	G	13: 31,558,812		probably benign	Het
Abca13	A	G	11: 9,292,306	T1390A	possibly damaging	Het
Abca14	T	A	7: 120,312,705		probably null	Het
Abca8a	A	C	11: 110,070,482	V538G	probably damaging	Het
Acy1	C	T	9: 106,433,583	G329R	probably benign	Het
Adamts17	T	C	7: 67,041,888	C607R	probably damaging	Het
Adamts20	A	T	15: 94,394,622	C202*	probably null	Het
Adcy5	A	G	16: 35,279,216	N712S	possibly damaging	Het
Ahnak	A	G	19: 9,004,681	K1110E	probably benign	Het
Anks6	T	A	4: 47,033,127	H578L	possibly damaging	Het
Appl1	C	A	14: 26,925,971	L626F	probably benign	Het
Arl1	A	G	10: 88,730,637		probably benign	Het
Atf4	T	A	15: 80,257,417	I336K	probably damaging	Het
Atp7b	A	T	8: 22,000,121	S1044T	probably benign	Het
B020031M17Rik	T	C	13: 119,949,842	Y76C	probably benign	Het
Carm1	A	G	9: 21,587,184	N466S	probably benign	Het
Cbl	A	G	9: 44,173,380	S153P	probably damaging	Het
Ccdc159	A	G	9: 21,927,731		probably null	Het
Cd109	CATTTATTTATTTATTTATTTATTTATTTATTTAT	CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT	9: 78,712,500		probably benign	Het
Cdc7	T	C	5: 106,973,841	F207L	probably benign	Het
Celsr2	T	C	3: 108,397,231	R2271G	probably benign	Het
Cep162	T	C	9: 87,206,862	Q989R	probably damaging	Het
Cep89	A	G	7: 35,438,437	T749A	probably benign	Het
Clcn5	T	C	X: 7,166,352		probably null	Het
Clu	A	T	14: 65,979,864	Y382F	probably benign	Het
Cnih4	A	G	1: 181,166,243		probably benign	Het
Crb1	A	G	1: 139,198,771	L1340P	probably damaging	Het
D730048I06Rik	A	T	9: 35,789,725	C22S	probably damaging	Het
Ddx4	T	C	13: 112,613,735	T421A	probably damaging	Het
Dennd5a	T	C	7: 109,921,198	E484G	probably benign	Het
Dsg4	G	T	18: 20,456,908	V372L	possibly damaging	Het
Dyrk2	T	C	10: 118,868,286	D21G	probably benign	Het
E2f1	C	G	2: 154,564,022	G144R	probably damaging	Het
Epb41l4a	A	T	18: 33,802,507		probably null	Het
F10	G	T	8: 13,039,621	V67F	possibly damaging	Het
Fat3	A	G	9: 16,031,173	I1301T	probably damaging	Het
Filip1l	A	G	16: 57,570,695	T549A	probably benign	Het
Flt4	C	A	11: 49,626,444		probably benign	Het
Fndc1	G	A	17: 7,771,480	T1128I	unknown	Het
Fos	T	C	12: 85,476,162	S283P	probably benign	Het
Fryl	T	C	5: 73,065,538	Y1900C	possibly damaging	Het
Fsip2	C	A	2: 82,987,029	Q4369K	probably benign	Het
Gad2	A	T	2: 22,673,970	H395L	probably damaging	Het
Grm2	T	A	9: 106,653,931	I120F	probably benign	Het
Hjurp	GT	GTT	1: 88,266,524		probably null	Het
Igsf10	A	T	3: 59,320,330	I1974N	probably damaging	Het
Il23r	T	C	6: 67,473,850	N215S	probably damaging	Het
Jph1	T	A	1: 17,091,704	M245L	possibly damaging	Het
Loxl4	G	A	19: 42,607,613	H147Y	probably benign	Het
Lsg1	A	G	16: 30,565,449	I521T	probably damaging	Het
Ltc4s	C	T	11: 50,237,081	G83R	probably damaging	Het
Map2	A	G	1: 66,410,637	E173G	probably damaging	Het
Med29	T	A	7: 28,386,927	D152V	possibly damaging	Het
Megf8	A	G	7: 25,363,515	D2432G	probably damaging	Het
Mrpl38	G	A	11: 116,135,152		probably benign	Het
Myh7	A	G	14: 54,988,321	I521T	possibly damaging	Het
Mylk	G	T	16: 34,922,435	V1106L	probably benign	Het
Myo15b	A	T	11: 115,861,935	D753V	possibly damaging	Het
Myo1g	T	C	11: 6,516,785		probably null	Het
Myrfl	A	G	10: 116,777,342		probably null	Het
Naip5	A	G	13: 100,223,414	V438A	possibly damaging	Het
Nav3	A	G	10: 109,764,935	V1277A	probably benign	Het
Nek10	T	A	14: 14,842,841	V182E	possibly damaging	Het
Ngly1	T	C	14: 16,281,809	V355A	probably benign	Het
Nol6	T	C	4: 41,118,944	E683G	possibly damaging	Het
Obsl1	A	T	1: 75,503,441	V487E	probably damaging	Het
Oc90	T	A	15: 65,881,505	R322W	possibly damaging	Het
Olfr1313	A	G	2: 112,071,752	V277A	possibly damaging	Het
Olfr357	C	A	2: 36,997,503	A231D	probably benign	Het
Olfr677	A	T	7: 105,056,276	H10L	possibly damaging	Het
Olfr878	A	G	9: 37,918,921	E93G	possibly damaging	Het
Osbp2	T	C	11: 3,712,160	H231R	probably damaging	Het
Pdzph1	T	C	17: 58,974,546	H247R	probably damaging	Het
Pidd1	T	C	7: 141,442,249	N209S	probably damaging	Het
Pknox1	C	T	17: 31,603,312	A351V	probably damaging	Het
Plxnd1	C	A	6: 115,958,615	V1737F	probably damaging	Het
Prkdc	A	T	16: 15,702,112	K1138M	probably damaging	Het
Rad54l2	T	C	9: 106,754,025	D21G	possibly damaging	Het
Recql4	C	T	15: 76,708,585	C302Y	probably damaging	Het
Scgb2b6	T	C	7: 31,619,483		noncoding transcript	Het
Slc10a5	C	A	3: 10,335,299	Q100H	probably damaging	Het
Slc10a5	T	G	3: 10,335,300	Q100P	probably damaging	Het
Slc5a9	A	T	4: 111,890,937	L226Q	possibly damaging	Het
Slfn1	T	C	11: 83,121,649	V197A	probably benign	Het
Spire1	T	C	18: 67,512,865	M244V	probably benign	Het
St3gal3	C	T	4: 117,960,035	V141I	probably benign	Het
St6galnac4	G	T	2: 32,587,160		probably benign	Het
Svep1	T	C	4: 58,097,323	K1407E	possibly damaging	Het
Tbc1d32	A	G	10: 56,224,649	C78R	probably damaging	Het
Tln2	A	G	9: 67,346,527	V754A	probably benign	Het
Tmeff1	A	T	4: 48,636,869	Y189F	possibly damaging	Het
Tmem131l	C	T	3: 83,899,212	A1433T	probably benign	Het
Tnfrsf8	T	C	4: 145,303,122	Y36C	probably damaging	Het
Trp53i11	G	T	2: 93,199,900	R184L	probably damaging	Het
Trpv1	A	T	11: 73,251,284	M214L	possibly damaging	Het
Tsnax	T	A	8: 125,028,794	S132T	probably benign	Het
Ttc28	T	C	5: 111,277,043	L1547P	probably damaging	Het
Ttc3	A	G	16: 94,439,241		probably null	Het
Tubal3	T	A	13: 3,933,514	D431E	probably damaging	Het
Ugt2b36	A	T	5: 87,092,442		probably null	Het
Vmn1r23	A	T	6: 57,926,205	I196K	probably benign	Het
Vmn1r55	A	C	7: 5,146,587	L279R	probably damaging	Het
Vmn1r55	G	T	7: 5,146,588	L279M	probably damaging	Het
Vmn2r89	G	A	14: 51,457,485	G474E	probably damaging	Het
Vps26b	T	C	9: 27,015,215	K163E	probably damaging	Het
Zfp142	A	G	1: 74,570,272	F1352L	probably damaging	Het
Zfp422	C	T	6: 116,626,883	E52K	possibly damaging	Het
Zfp423	T	A	8: 87,781,710		probably null	Het
Zfp493	T	C	13: 67,786,617	F230L	probably damaging	Het
Zfp760	T	C	17: 21,722,407	C188R	probably benign	Het
Zfyve28	G	T	5: 34,217,845	T275K	probably damaging	Het
Znhit3	T	C	11: 84,916,329	N5D	probably benign	Het

Other mutations in Sdc1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00090:Sdc1	APN	12	8790459	missense	possibly damaging	0.75
IGL02197:Sdc1	APN	12	8790835	missense	possibly damaging	0.90
E0374:Sdc1	UTSW	12	8789424	missense	probably damaging	1.00
R1673:Sdc1	UTSW	12	8790409	missense	possibly damaging	0.66
R4887:Sdc1	UTSW	12	8791708	missense	probably damaging	1.00
R5396:Sdc1	UTSW	12	8791743	unclassified	probably null
R6358:Sdc1	UTSW	12	8791297	missense	probably damaging	0.99
R7272:Sdc1	UTSW	12	8790554	missense	probably benign	0.41
R7575:Sdc1	UTSW	12	8790619	missense	probably damaging	1.00
R7741:Sdc1	UTSW	12	8791370	missense	probably benign	0.06

Predicted Primers

PCR Primer
(F):5'- AGAGCATGAATCACGTCAGG -3'
(R):5'- TTGATGACAGAAGTGCCGC -3'

Sequencing Primer
(F):5'- TGATGCCTGGAGACCTCTC -3'
(R):5'- TCTCATGGAGGCCAGGTTGC -3'

Posted On

2015-10-21