Incidental Mutation 'R1673:Sdc1'
ID 187842
Institutional Source Beutler Lab
Gene Symbol Sdc1
Ensembl Gene ENSMUSG00000020592
Gene Name syndecan 1
Synonyms CD138, syn-1, Synd, Synd1
MMRRC Submission 039709-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.260) question?
Stock # R1673 (G1)
Quality Score 184
Status Not validated
Chromosome 12
Chromosomal Location 8821396-8843716 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 8840409 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Glutamine at position 62 (R62Q)
Ref Sequence ENSEMBL: ENSMUSP00000123896 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020911] [ENSMUST00000161883] [ENSMUST00000171158]
AlphaFold P18828
Predicted Effect probably benign
Transcript: ENSMUST00000020911
AA Change: R58Q

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000020911
Gene: ENSMUSG00000020592
AA Change: R58Q

DomainStartEndE-ValueType
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: R62Q

PolyPhen 2 Score 0.663 (Sensitivity: 0.86; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000123896
Gene: ENSMUSG00000020592
AA Change: R62Q

DomainStartEndE-ValueType
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: R58Q

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000131491
Gene: ENSMUSG00000020592
AA Change: R58Q

DomainStartEndE-ValueType
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
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.1%
  • 20x: 91.9%
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 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: 80 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca6 T C 11: 110,103,165 (GRCm39) S809G probably benign Het
Ap4b1 T A 3: 103,725,161 (GRCm39) probably null Het
Aqp12 A G 1: 92,934,606 (GRCm39) Q161R possibly damaging Het
Atp8a2 A G 14: 60,028,689 (GRCm39) I926T probably benign Het
Cacna2d1 A T 5: 16,504,988 (GRCm39) N314I probably damaging Het
Cd209d A G 8: 3,927,113 (GRCm39) S81P probably damaging Het
Cdcp1 T A 9: 123,007,086 (GRCm39) K554* probably null Het
Celsr1 A G 15: 85,816,658 (GRCm39) Y1762H probably benign Het
Cklf A G 8: 104,983,983 (GRCm39) T49A possibly damaging Het
Col12a1 T G 9: 79,600,820 (GRCm39) I755L probably benign Het
Cts3 G A 13: 61,715,368 (GRCm39) Q140* probably null Het
Ddx1 A T 12: 13,294,967 (GRCm39) probably null Het
Dnah3 C A 7: 119,570,402 (GRCm39) E2262* probably null Het
Dnah5 A G 15: 28,290,294 (GRCm39) N1228S probably benign Het
Dsg1a G A 18: 20,464,561 (GRCm39) R352Q probably damaging Het
Efcab5 A G 11: 77,042,679 (GRCm39) F25L probably damaging Het
Efhd1 T A 1: 87,192,404 (GRCm39) V78D probably damaging Het
Eif5a2 T C 3: 28,847,967 (GRCm39) probably null Het
Elp2 T A 18: 24,744,983 (GRCm39) V101D possibly damaging Het
Enpp2 A T 15: 54,773,592 (GRCm39) probably null Het
F5 A G 1: 164,007,089 (GRCm39) T298A probably damaging Het
Fbxo21 G T 5: 118,146,129 (GRCm39) R584L probably benign Het
Fbxw22 G T 9: 109,211,196 (GRCm39) F368L possibly damaging Het
Gcn1 T C 5: 115,720,356 (GRCm39) I409T probably benign Het
Gm12887 T C 4: 121,473,655 (GRCm39) Y65C probably damaging Het
Gria4 G A 9: 4,537,637 (GRCm39) Q224* probably null Het
Hdac5 C T 11: 102,089,631 (GRCm39) V860M probably damaging Het
Ino80 G A 2: 119,212,417 (GRCm39) R1302C probably damaging Het
Kcns2 A T 15: 34,838,966 (GRCm39) I110F probably damaging Het
Lrig3 A G 10: 125,846,036 (GRCm39) T822A probably damaging Het
Mapk6 T C 9: 75,302,851 (GRCm39) D214G probably damaging Het
Mcm2 A T 6: 88,869,060 (GRCm39) L264Q probably benign Het
Mpnd A T 17: 56,317,455 (GRCm39) Y64F probably damaging Het
Muc1 T A 3: 89,139,079 (GRCm39) M520K possibly damaging Het
Muc4 T A 16: 32,577,276 (GRCm39) S189T probably benign Het
Myh13 T C 11: 67,242,945 (GRCm39) S953P possibly damaging Het
Ncf2 A T 1: 152,706,230 (GRCm39) M281L probably benign Het
Nipal2 A G 15: 34,648,841 (GRCm39) I116T probably damaging Het
Nptn T C 9: 58,531,015 (GRCm39) L46P probably benign Het
Or2b6 A T 13: 21,823,214 (GRCm39) S160T probably damaging Het
Or4k77 A G 2: 111,199,552 (GRCm39) T192A probably benign Het
Or51ag1 C A 7: 103,155,896 (GRCm39) V86F probably damaging Het
Or5ae1 T A 7: 84,565,325 (GRCm39) F113I probably damaging Het
Pgr A T 9: 8,902,069 (GRCm39) Y534F possibly damaging Het
Pip4k2a A T 2: 18,877,093 (GRCm39) probably null Het
Pkd1l2 C G 8: 117,767,514 (GRCm39) V1259L probably benign Het
Ppp1r12a A G 10: 108,085,426 (GRCm39) E457G probably damaging Het
Rasa4 T A 5: 136,133,491 (GRCm39) V650D probably benign Het
Rem2 C T 14: 54,713,766 (GRCm39) probably benign Het
Rps18-ps6 A T 13: 97,896,868 (GRCm39) Y77N possibly damaging Het
Sdk1 A G 5: 141,934,261 (GRCm39) E366G possibly damaging Het
Setd2 T A 9: 110,433,248 (GRCm39) H2406Q probably damaging Het
Slc30a5 A G 13: 100,949,891 (GRCm39) V397A probably benign Het
Slc36a2 A T 11: 55,075,739 (GRCm39) L16H possibly damaging Het
Slc44a1 T C 4: 53,542,468 (GRCm39) V334A probably benign Het
Sox8 A T 17: 25,786,456 (GRCm39) Y416N possibly damaging Het
Speg T C 1: 75,387,807 (GRCm39) V1416A possibly damaging Het
Stimate T C 14: 30,586,391 (GRCm39) L72S possibly damaging Het
Stk24 T A 14: 121,574,983 (GRCm39) I42F probably damaging Het
Tasor2 A G 13: 3,634,498 (GRCm39) probably null Het
Tcerg1 T A 18: 42,685,646 (GRCm39) L661Q possibly damaging Het
Tpp1 G A 7: 105,396,880 (GRCm39) R417W probably damaging Het
Trim12a T A 7: 103,955,264 (GRCm39) D153V possibly damaging Het
Trpm2 T C 10: 77,778,778 (GRCm39) N396S probably benign Het
Ttn T C 2: 76,637,427 (GRCm39) K5695R probably damaging Het
Ttn G A 2: 76,640,631 (GRCm39) R11960C probably damaging Het
Tulp3 A C 6: 128,310,906 (GRCm39) probably null Het
Uaca T A 9: 60,779,438 (GRCm39) L1273H probably damaging Het
Usp33 A G 3: 152,073,919 (GRCm39) E255G probably damaging Het
Vmn2r54 T G 7: 12,350,138 (GRCm39) probably null Het
Vwa8 C T 14: 79,145,670 (GRCm39) R116C probably damaging Het
Wnt5b A T 6: 119,423,315 (GRCm39) F116L probably benign Het
Zbtb12 CTTCAT CTTCATTCAT 17: 35,115,284 (GRCm39) probably null Het
Zbtb12 TCATC TCATCCATC 17: 35,115,286 (GRCm39) probably null Het
Zfp408 G A 2: 91,476,353 (GRCm39) T367I probably damaging Het
Zfp512b G A 2: 181,230,286 (GRCm39) A480V possibly damaging Het
Zfp560 T C 9: 20,258,949 (GRCm39) T638A probably benign Het
Zfp932 G T 5: 110,156,854 (GRCm39) G151V probably damaging Het
Zpbp T C 11: 11,302,696 (GRCm39) K320E probably damaging Het
Zranb2 C T 3: 157,243,277 (GRCm39) P91L probably damaging Het
Other mutations in Sdc1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00090:Sdc1 APN 12 8,840,459 (GRCm39) missense possibly damaging 0.75
IGL02197:Sdc1 APN 12 8,840,835 (GRCm39) missense possibly damaging 0.90
E0374:Sdc1 UTSW 12 8,839,424 (GRCm39) missense probably damaging 1.00
R4700:Sdc1 UTSW 12 8,840,541 (GRCm39) missense possibly damaging 0.82
R4887:Sdc1 UTSW 12 8,841,708 (GRCm39) missense probably damaging 1.00
R5396:Sdc1 UTSW 12 8,841,743 (GRCm39) splice site probably null
R6358:Sdc1 UTSW 12 8,841,297 (GRCm39) missense probably damaging 0.99
R7272:Sdc1 UTSW 12 8,840,554 (GRCm39) missense probably benign 0.41
R7575:Sdc1 UTSW 12 8,840,619 (GRCm39) missense probably damaging 1.00
R7741:Sdc1 UTSW 12 8,841,370 (GRCm39) missense probably benign 0.06
R8125:Sdc1 UTSW 12 8,840,663 (GRCm39) missense probably benign 0.01
R8900:Sdc1 UTSW 12 8,840,460 (GRCm39) missense possibly damaging 0.92
R9096:Sdc1 UTSW 12 8,841,665 (GRCm39) missense probably damaging 1.00
R9225:Sdc1 UTSW 12 8,821,817 (GRCm39) missense unknown
Predicted Primers PCR Primer
(F):5'- AGCCTTTGCTAGGTCACCTTTGGG -3'
(R):5'- TCTTTGATGACAGAAGTGCCGCC -3'

Sequencing Primer
(F):5'- GGGTCTCAGAAGGCTTCAG -3'
(R):5'- CTTGTCCCGAGCAGTGAAG -3'
Posted On 2014-05-09