Incidental Mutation 'R2875:Sdc4'
ID 260502
Institutional Source Beutler Lab
Gene Symbol Sdc4
Ensembl Gene ENSMUSG00000017009
Gene Name syndecan 4
Synonyms Synd4, ryudocan, S4, syndecan-4
MMRRC Submission 040463-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R2875 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 164266167-164285512 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 164273211 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 33 (D33G)
Ref Sequence ENSEMBL: ENSMUSP00000017153 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000017153]
AlphaFold O35988
Predicted Effect possibly damaging
Transcript: ENSMUST00000017153
AA Change: D33G

PolyPhen 2 Score 0.918 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000017153
Gene: ENSMUSG00000017009
AA Change: D33G

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
4.1m 169 187 1.61e-3 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142909
Meta Mutation Damage Score 0.0789 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.3%
Validation Efficiency 100% (1/1)
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 that functions as a receptor in intracellular signaling. The encoded protein is found as a homodimer and is a member of the syndecan proteoglycan family. This gene is found on chromosome 20, while a pseudogene has been found on chromosome 22. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous or heterozygous for a knock-out allele show delayed wound healing and impaired angiogenesis. Homozygotes for a different knock-out allele exhibit degenerated fetal vessels in the placental labyrinth, abnormal cell adhesion, and high susceptibility to induced renal and hepatic injury. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 36 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam34l T A 8: 44,080,177 (GRCm39) K16* probably null Het
Adgb T G 10: 10,298,463 (GRCm39) T422P probably damaging Het
Adrm1 A G 2: 179,817,411 (GRCm39) T293A probably damaging Het
Baz1a A T 12: 54,969,904 (GRCm39) D585E probably damaging Het
Ccdc152 T C 15: 3,327,663 (GRCm39) N38S probably damaging Het
Cenpf A G 1: 189,390,841 (GRCm39) M997T probably benign Het
Dnah12 A G 14: 26,414,625 (GRCm39) I9V probably benign Het
Dnah12 A G 14: 26,598,907 (GRCm39) N995S probably benign Het
Dnah9 C A 11: 66,059,287 (GRCm39) G3C possibly damaging Het
Dock2 A G 11: 34,609,712 (GRCm39) S243P probably damaging Het
Eif2ak3 T C 6: 70,860,623 (GRCm39) S400P probably damaging Het
Eno1b A G 18: 48,180,851 (GRCm39) K343R possibly damaging Het
Grk6 A G 13: 55,600,117 (GRCm39) H271R probably damaging Het
H2-Ab1 A C 17: 34,482,286 (GRCm39) M1L probably benign Het
Irf8 C A 8: 121,481,202 (GRCm39) P262Q probably damaging Het
Kcnc3 G T 7: 44,240,961 (GRCm39) G218* probably null Het
Krt9 C A 11: 100,080,031 (GRCm39) G454* probably null Het
Mgrn1 C T 16: 4,725,280 (GRCm39) T47I possibly damaging Het
Ndst1 A T 18: 60,823,119 (GRCm39) F816I probably damaging Het
Or11g26 T A 14: 50,753,269 (GRCm39) W203R probably benign Het
Or5h25 A T 16: 58,930,165 (GRCm39) D269E probably benign Het
Phf12 C A 11: 77,900,573 (GRCm39) T223N probably damaging Het
Rad1 T C 15: 10,490,417 (GRCm39) V128A probably benign Het
Rad54l C T 4: 115,959,050 (GRCm39) R382Q probably benign Het
Rhbdd1 A G 1: 82,346,090 (GRCm39) D215G probably benign Het
Smarca4 A T 9: 21,553,876 (GRCm39) K387N possibly damaging Het
St3gal5 A G 6: 72,124,114 (GRCm39) M214V possibly damaging Het
Stk25 T C 1: 93,556,973 (GRCm39) D15G possibly damaging Het
Timm21 T C 18: 84,969,217 (GRCm39) D69G probably benign Het
Ttll4 A G 1: 74,725,597 (GRCm39) probably null Het
Ttn T A 2: 76,589,438 (GRCm39) N21272I probably damaging Het
Uchl3 A G 14: 101,905,996 (GRCm39) H153R probably benign Het
Zbed6 C T 1: 133,584,598 (GRCm39) C913Y probably damaging Het
Zcwpw1 T C 5: 137,808,304 (GRCm39) S251P probably damaging Het
Zeb1 GGA GGAAGA 18: 5,772,859 (GRCm39) probably benign Het
Zscan29 T C 2: 120,994,581 (GRCm39) Y468C probably damaging Het
Other mutations in Sdc4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01889:Sdc4 APN 2 164,273,127 (GRCm39) missense probably damaging 1.00
Jiangxi UTSW 2 164,273,206 (GRCm39) missense probably benign 0.30
R1724:Sdc4 UTSW 2 164,273,206 (GRCm39) missense probably benign 0.30
R1839:Sdc4 UTSW 2 164,270,932 (GRCm39) missense probably benign 0.01
R2876:Sdc4 UTSW 2 164,273,211 (GRCm39) missense possibly damaging 0.92
R4833:Sdc4 UTSW 2 164,273,138 (GRCm39) missense probably damaging 0.96
R6250:Sdc4 UTSW 2 164,273,138 (GRCm39) missense probably damaging 0.96
R8770:Sdc4 UTSW 2 164,270,822 (GRCm39) missense probably damaging 1.00
R9087:Sdc4 UTSW 2 164,270,959 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- GCACTGTAGGAAAATGTCGACTC -3'
(R):5'- GACTTGTATAGGGTTGCACAGTAG -3'

Sequencing Primer
(F):5'- CTGTAGGAAAATGTCGACTCAAATCC -3'
(R):5'- TTGCACAGTAGATGGGGCAC -3'
Posted On 2015-01-23