Incidental Mutation 'R2876:Sdc4'
ID 260545
Institutional Source Beutler Lab
Gene Symbol Sdc4
Ensembl Gene ENSMUSG00000017009
Gene Name syndecan 4
Synonyms Synd4, ryudocan, S4, syndecan-4
MMRRC Submission 040464-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R2876 (G1)
Quality Score 225
Status 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: 97.3%
  • 20x: 95.2%
Validation Efficiency 95% (42/44)
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: 40 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
5730507C01Rik C A 12: 18,583,644 (GRCm39) Q235K possibly damaging Het
Abcc1 A T 16: 14,275,824 (GRCm39) H906L probably benign Het
Acot6 T G 12: 84,148,036 (GRCm39) D97E possibly damaging Het
Acvr2a T A 2: 48,782,190 (GRCm39) M241K probably damaging Het
Adamts9 T C 6: 92,772,891 (GRCm39) probably benign 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
Ankfn1 A G 11: 89,282,462 (GRCm39) V395A possibly damaging Het
Atp2b1 A G 10: 98,835,607 (GRCm39) M451V probably damaging Het
Ccdc152 T C 15: 3,327,663 (GRCm39) N38S probably damaging Het
Cdh23 A T 10: 60,143,275 (GRCm39) N3017K probably damaging Het
Cenpf A G 1: 189,390,841 (GRCm39) M997T probably benign Het
Gcc2 A G 10: 58,126,124 (GRCm39) E1344G probably damaging Het
Gen1 A C 12: 11,292,069 (GRCm39) S573R probably benign Het
Ilvbl C A 10: 78,418,890 (GRCm39) Q410K probably benign Het
Ints11 C A 4: 155,971,882 (GRCm39) probably benign Het
Itfg1 T C 8: 86,507,139 (GRCm39) probably benign Het
Lrrc27 C T 7: 138,808,600 (GRCm39) probably benign Het
Maml3 G A 3: 51,597,480 (GRCm39) A422V possibly damaging Het
Masp2 T A 4: 148,692,458 (GRCm39) I317K probably benign Het
Or13n4 A T 7: 106,423,664 (GRCm39) V23E probably benign Het
Or2ag18 C G 7: 106,405,204 (GRCm39) S155T probably benign Het
Or5g26 A G 2: 85,494,034 (GRCm39) V248A probably damaging Het
Papln T A 12: 83,825,701 (GRCm39) S661T probably damaging Het
Pi4ka A G 16: 17,185,414 (GRCm39) S229P possibly damaging Het
Piezo2 A G 18: 63,186,106 (GRCm39) S1688P probably damaging Het
Pzp T C 6: 128,468,513 (GRCm39) T1005A probably damaging Het
Rad1 T C 15: 10,490,417 (GRCm39) V128A probably benign Het
Rhbdd1 A G 1: 82,346,090 (GRCm39) D215G probably benign Het
Rnft2 G A 5: 118,331,686 (GRCm39) R417C probably damaging Het
Scn2a A C 2: 65,546,241 (GRCm39) I935L possibly damaging Het
Slco1c1 T C 6: 141,505,582 (GRCm39) S454P probably damaging Het
Spidr A T 16: 15,730,453 (GRCm39) probably null Het
Srp72 T A 5: 77,143,767 (GRCm39) probably benign Het
Ttll4 A G 1: 74,725,597 (GRCm39) probably null Het
Ttn C T 2: 76,750,684 (GRCm39) S3455N probably damaging Het
Vcan T A 13: 89,852,356 (GRCm39) E868V probably damaging Het
Vmn2r89 G T 14: 51,692,541 (GRCm39) G115C possibly damaging Het
Zbed6 C T 1: 133,584,598 (GRCm39) C913Y probably damaging 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
R2875: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'- ACTTGTATAGGGTTGCACAGTAG -3'

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