Incidental Mutation 'R6358:Sdc1'
ID 513352
Institutional Source Beutler Lab
Gene Symbol Sdc1
Ensembl Gene ENSMUSG00000020592
Gene Name syndecan 1
Synonyms CD138, syn-1, Synd, Synd1
MMRRC Submission 044508-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.260) question?
Stock # R6358 (G1)
Quality Score 139.008
Status Validated
Chromosome 12
Chromosomal Location 8821396-8843716 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 8841297 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Proline at position 213 (T213P)
Ref Sequence ENSEMBL: ENSMUSP00000131491 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020911] [ENSMUST00000161883] [ENSMUST00000171158]
AlphaFold P18828
Predicted Effect probably damaging
Transcript: ENSMUST00000020911
AA Change: T213P

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000020911
Gene: ENSMUSG00000020592
AA Change: T213P

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 probably benign
Transcript: ENSMUST00000161883
SMART Domains Protein: ENSMUSP00000123896
Gene: ENSMUSG00000020592

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 damaging
Transcript: ENSMUST00000171158
AA Change: T213P

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000131491
Gene: ENSMUSG00000020592
AA Change: T213P

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
Meta Mutation Damage Score 0.1384 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.2%
  • 20x: 94.8%
Validation Efficiency 100% (61/61)
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam39 T C 8: 41,279,718 (GRCm39) V703A probably benign Het
Adgrv1 T A 13: 81,562,702 (GRCm39) Q5389L probably damaging Het
Aldh18a1 A T 19: 40,566,122 (GRCm39) I42N possibly damaging Het
Ankrd28 A C 14: 31,432,821 (GRCm39) C575W probably damaging Het
Car14 T A 3: 95,805,487 (GRCm39) T329S possibly damaging Het
Cdhr2 T C 13: 54,884,359 (GRCm39) F1298S probably damaging Het
Crhr2 A G 6: 55,070,028 (GRCm39) I341T probably benign Het
D5Ertd579e T A 5: 36,773,580 (GRCm39) probably null Het
Eif1ad3 A G 12: 87,843,770 (GRCm39) E139G unknown Het
Emilin1 A G 5: 31,075,562 (GRCm39) E601G probably damaging Het
Erbin T A 13: 103,982,073 (GRCm39) Q456L probably damaging Het
Glp1r T C 17: 31,151,618 (GRCm39) V405A probably benign Het
Gm10220 C G 5: 26,325,303 (GRCm39) probably null Het
Gm527 A T 12: 64,970,322 (GRCm39) H219L possibly damaging Het
Gorasp2 T A 2: 70,503,104 (GRCm39) M1K probably null Het
H2-DMa T A 17: 34,356,958 (GRCm39) L152H probably damaging Het
Hsd3b7 T A 7: 127,400,709 (GRCm39) H54Q probably damaging Het
Hspa12b T C 2: 130,978,986 (GRCm39) probably benign Het
Iars1 C A 13: 49,880,619 (GRCm39) T1006K possibly damaging Het
Jmjd1c T C 10: 67,061,718 (GRCm39) V1357A probably benign Het
Magi3 T C 3: 103,958,268 (GRCm39) M606V probably damaging Het
Mia T C 7: 26,880,403 (GRCm39) D24G probably benign Het
Mon2 A T 10: 122,849,409 (GRCm39) L1297Q probably damaging Het
Musk T A 4: 58,373,171 (GRCm39) S691T possibly damaging Het
Myo5c A T 9: 75,203,294 (GRCm39) E1463D possibly damaging Het
Ndufs6 C T 13: 73,468,438 (GRCm39) G87D probably damaging Het
Npnt C T 3: 132,610,479 (GRCm39) V415I probably benign Het
Ntsr2 A G 12: 16,706,769 (GRCm39) I266V probably benign Het
Or11j4 A T 14: 50,630,845 (GRCm39) I211F possibly damaging Het
Or5aq7 T C 2: 86,938,778 (GRCm39) probably benign Het
Pkmyt1 T A 17: 23,952,630 (GRCm39) probably null Het
Polr1e T C 4: 45,026,813 (GRCm39) L166P probably damaging Het
Ppib T G 9: 65,968,756 (GRCm39) F48C probably damaging Het
Ppl C A 16: 4,905,793 (GRCm39) E1501* probably null Het
Prpf8 T C 11: 75,382,321 (GRCm39) V384A probably benign Het
Ptch1 T G 13: 63,661,503 (GRCm39) S1212R probably damaging Het
Ralb C A 1: 119,403,735 (GRCm39) D131Y probably damaging Het
Rfx4 T A 10: 84,680,099 (GRCm39) M141K probably damaging Het
Rgl2 T A 17: 34,156,105 (GRCm39) probably null Het
Rpl27 A G 11: 101,334,782 (GRCm39) probably benign Het
Setx T A 2: 29,061,360 (GRCm39) N2256K possibly damaging Het
Shank2 A G 7: 143,585,034 (GRCm39) M12V probably benign Het
Slc22a28 T A 19: 8,049,253 (GRCm39) K332M probably damaging Het
Slf2 A T 19: 44,923,864 (GRCm39) H226L probably benign Het
Tbc1d10b T C 7: 126,802,584 (GRCm39) S362G probably benign Het
Tbxas1 G A 6: 38,929,046 (GRCm39) probably benign Het
Tctn1 A G 5: 122,399,575 (GRCm39) V83A probably damaging Het
Tgm4 A G 9: 122,885,583 (GRCm39) E375G probably damaging Het
Tmeff2 T A 1: 51,172,273 (GRCm39) Y247* probably null Het
Tmem167b C T 3: 108,466,211 (GRCm39) R79H possibly damaging Het
Tmprss7 T G 16: 45,489,936 (GRCm39) M429L probably benign Het
Tnfsf18 T A 1: 161,331,148 (GRCm39) D99E probably benign Het
Tnrc18 A T 5: 142,713,736 (GRCm39) S2534T probably damaging Het
Tnxb A G 17: 34,897,968 (GRCm39) E872G probably damaging Het
Tomm40l C T 1: 171,047,206 (GRCm39) V237I possibly damaging Het
Trbv2 A G 6: 41,024,836 (GRCm39) Q84R probably benign Het
Tspan18 T C 2: 93,040,219 (GRCm39) R179G probably benign Het
Tspan8 G T 10: 115,669,132 (GRCm39) V56L probably benign Het
Zbtb22 T C 17: 34,137,711 (GRCm39) S619P probably damaging Het
Zfp2 A T 11: 50,791,428 (GRCm39) I205N probably damaging Het
Zfpm1 A G 8: 123,063,850 (GRCm39) probably benign 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
R1673:Sdc1 UTSW 12 8,840,409 (GRCm39) missense possibly damaging 0.66
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
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'- TACGTTGTGTCACTGGAGGC -3'
(R):5'- TGCTGCTAAAGATGCTTCACCC -3'

Sequencing Primer
(F):5'- TGTCACTGGAGGCGGTATC -3'
(R):5'- GGCTACCTCAGAGCCACC -3'
Posted On 2018-04-27