Incidental Mutation 'R4779:Sdc3'
ID 368134
Institutional Source Beutler Lab
Gene Symbol Sdc3
Ensembl Gene ENSMUSG00000025743
Gene Name syndecan 3
Synonyms syn-3, Synd3
MMRRC Submission 045240-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.135) question?
Stock # R4779 (G1)
Quality Score 225
Status Validated
Chromosome 4
Chromosomal Location 130519848-130553629 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 130546376 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Leucine at position 245 (P245L)
Ref Sequence ENSEMBL: ENSMUSP00000065877 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000070478] [ENSMUST00000141297] [ENSMUST00000152591]
AlphaFold Q64519
Predicted Effect probably damaging
Transcript: ENSMUST00000070478
AA Change: P245L

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000065877
Gene: ENSMUSG00000025743
AA Change: P245L

DomainStartEndE-ValueType
signal peptide 1 44 N/A INTRINSIC
low complexity region 60 76 N/A INTRINSIC
low complexity region 101 115 N/A INTRINSIC
low complexity region 123 154 N/A INTRINSIC
low complexity region 157 202 N/A INTRINSIC
low complexity region 213 240 N/A INTRINSIC
low complexity region 276 287 N/A INTRINSIC
low complexity region 330 341 N/A INTRINSIC
4.1m 408 426 2.51e-5 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140623
Predicted Effect probably benign
Transcript: ENSMUST00000141297
SMART Domains Protein: ENSMUSP00000123608
Gene: ENSMUSG00000025743

DomainStartEndE-ValueType
low complexity region 7 21 N/A INTRINSIC
low complexity region 29 60 N/A INTRINSIC
low complexity region 63 108 N/A INTRINSIC
low complexity region 119 146 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146093
Predicted Effect probably benign
Transcript: ENSMUST00000152591
SMART Domains Protein: ENSMUSP00000118685
Gene: ENSMUSG00000025743

DomainStartEndE-ValueType
low complexity region 7 21 N/A INTRINSIC
low complexity region 29 60 N/A INTRINSIC
low complexity region 63 108 N/A INTRINSIC
low complexity region 119 146 N/A INTRINSIC
Meta Mutation Damage Score 0.1223 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.8%
Validation Efficiency 98% (95/97)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene belongs to the syndecan proteoglycan family. It may play a role in the organization of cell shape by affecting the actin cytoskeleton, possibly by transferring signals from the cell surface in a sugar-dependent mechanism. Allelic variants of this gene have been associated with obesity. [provided by RefSeq, Oct 2009]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit enhanced long-term potentiation and impaired hippocampus-dependent memory. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 87 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930562C15Rik T A 16: 4,667,613 (GRCm39) S335T unknown Het
4933421I07Rik T A 7: 42,097,455 (GRCm39) H13L possibly damaging Het
6030468B19Rik A G 11: 117,696,834 (GRCm39) T185A probably benign Het
Abcc1 T A 16: 14,228,635 (GRCm39) V294E probably benign Het
Abhd16b A G 2: 181,135,253 (GRCm39) T52A possibly damaging Het
Actl7a A T 4: 56,743,632 (GRCm39) N53I probably benign Het
Ankmy1 T C 1: 92,814,445 (GRCm39) E354G probably benign Het
Arap1 T C 7: 101,053,574 (GRCm39) F1301S probably damaging Het
Arfgef1 A T 1: 10,223,958 (GRCm39) W1447R probably damaging Het
Atoh7 ATGGCGCT AT 10: 62,936,187 (GRCm39) probably benign Het
Ccl24 T A 5: 135,601,811 (GRCm39) T6S possibly damaging Het
Cep152 G T 2: 125,410,812 (GRCm39) P1292Q possibly damaging Het
Cfap46 T C 7: 139,239,731 (GRCm39) probably benign Het
Chd6 A T 2: 160,791,477 (GRCm39) S2627T probably damaging Het
Chd8 A T 14: 52,468,963 (GRCm39) S552T probably damaging Het
Ciita C A 16: 10,329,230 (GRCm39) L502M probably damaging Het
Clic1 T C 17: 35,271,463 (GRCm39) F31S probably damaging Het
Cntnap1 T A 11: 101,068,898 (GRCm39) I147N possibly damaging Het
Cplane1 T C 15: 8,248,322 (GRCm39) S1624P probably benign Het
Crispld1 T A 1: 17,819,831 (GRCm39) D276E probably benign Het
Cspg4 A T 9: 56,793,092 (GRCm39) N276Y probably damaging Het
Cspg4b A T 13: 113,504,870 (GRCm39) N2000Y possibly damaging Het
Cwf19l2 A G 9: 3,410,035 (GRCm39) M55V possibly damaging Het
Cyp2c69 T C 19: 39,866,038 (GRCm39) N185S probably benign Het
Dop1b T C 16: 93,553,969 (GRCm39) I301T probably damaging Het
Epg5 T C 18: 78,034,580 (GRCm39) V1443A probably benign Het
Ephb4 T C 5: 137,363,964 (GRCm39) V612A probably benign Het
Fcgbp T A 7: 27,794,362 (GRCm39) C1189S probably damaging Het
Fgfr2 T G 7: 129,786,923 (GRCm39) probably benign Het
Fmn2 A G 1: 174,437,461 (GRCm39) E1144G probably damaging Het
Fmo3 T C 1: 162,796,407 (GRCm39) Y55C probably damaging Het
Frmpd1 A G 4: 45,229,865 (GRCm39) T11A probably damaging Het
Ghdc G T 11: 100,660,929 (GRCm39) Q79K possibly damaging Het
Gm11677 C T 11: 111,615,537 (GRCm39) noncoding transcript Het
Gm5591 T C 7: 38,221,680 (GRCm39) T130A probably damaging Het
Heg1 T G 16: 33,540,142 (GRCm39) D367E probably benign Het
Igkv13-84 C T 6: 68,916,894 (GRCm39) P64S probably damaging Het
Il10rb T A 16: 91,211,545 (GRCm39) S128T possibly damaging Het
Il15ra T A 2: 11,723,117 (GRCm39) I47N probably damaging Het
Il33 C A 19: 29,936,311 (GRCm39) S207* probably null Het
Itgb7 A G 15: 102,132,848 (GRCm39) Y155H possibly damaging Het
Kdm5a A G 6: 120,346,060 (GRCm39) probably benign Het
Kif11 G A 19: 37,406,397 (GRCm39) V987I probably benign Het
Krtap19-2 G A 16: 88,670,762 (GRCm39) probably benign Het
Krtap24-1 T A 16: 88,408,417 (GRCm39) R236S probably damaging Het
L3mbtl2 A G 15: 81,566,813 (GRCm39) I406V probably benign Het
Lrp2 A T 2: 69,290,059 (GRCm39) H3593Q possibly damaging Het
Mavs G T 2: 131,082,285 (GRCm39) W56C probably damaging Het
Mn1 C T 5: 111,567,526 (GRCm39) P499S probably damaging Het
Ntn5 T A 7: 45,340,895 (GRCm39) C178S probably damaging Het
Nufip2 A G 11: 77,577,154 (GRCm39) H34R unknown Het
Or5p51 T A 7: 107,444,755 (GRCm39) M62L possibly damaging Het
Or6f2 T A 7: 139,756,363 (GRCm39) L110Q probably damaging Het
Osbpl10 C T 9: 114,938,598 (GRCm39) S86L probably damaging Het
Pitpna T A 11: 75,511,153 (GRCm39) M242K possibly damaging Het
Pnpla6 T C 8: 3,572,838 (GRCm39) V345A probably benign Het
Polk A G 13: 96,632,999 (GRCm39) probably null Het
Polr3k A G 2: 181,506,340 (GRCm39) Y30C probably damaging Het
Pramel6 A G 2: 87,339,941 (GRCm39) H235R probably benign Het
Ptpra G A 2: 130,379,537 (GRCm39) V364I probably damaging Het
Recql A G 6: 142,309,426 (GRCm39) probably benign Het
Ring1 T C 17: 34,241,263 (GRCm39) probably benign Het
Rufy4 T C 1: 74,186,822 (GRCm39) C537R probably damaging Het
Samsn1 C A 16: 75,744,177 (GRCm39) noncoding transcript Het
Scara5 A G 14: 65,968,198 (GRCm39) H157R probably benign Het
Slc18b1 T A 10: 23,696,767 (GRCm39) M318K possibly damaging Het
Slc26a10 C T 10: 127,009,224 (GRCm39) A638T possibly damaging Het
Slc35f2 T A 9: 53,717,013 (GRCm39) W259R possibly damaging Het
Spata13 G A 14: 60,991,356 (GRCm39) W366* probably null Het
Sptlc3 A G 2: 139,431,509 (GRCm39) T344A probably benign Het
Tap1 T C 17: 34,412,865 (GRCm39) V560A probably damaging Het
Tbc1d1 T C 5: 64,435,389 (GRCm39) probably null Het
Tlr11 A G 14: 50,598,707 (GRCm39) Y231C possibly damaging Het
Tmem245 A T 4: 56,936,468 (GRCm39) S230T possibly damaging Het
Tnnt3 C T 7: 142,068,020 (GRCm39) probably benign Het
Traf7 C G 17: 24,729,412 (GRCm39) probably benign Het
Tshz2 A G 2: 169,804,601 (GRCm39) probably benign Het
Tshz3 T C 7: 36,468,397 (GRCm39) S129P probably damaging Het
Ttc6 A T 12: 57,776,237 (GRCm39) N1727I probably damaging Het
Ttc7b A G 12: 100,369,621 (GRCm39) S383P probably damaging Het
Tulp3 T A 6: 128,300,083 (GRCm39) I448F probably damaging Het
Ube3b T C 5: 114,542,778 (GRCm39) probably null Het
Vav1 G A 17: 57,603,552 (GRCm39) V84I probably damaging Het
Vav3 A T 3: 109,416,110 (GRCm39) K243I possibly damaging Het
Vmn1r25 T A 6: 57,956,011 (GRCm39) I93F probably damaging Het
Vmn2r73 C T 7: 85,520,923 (GRCm39) W348* probably null Het
Zdbf2 A G 1: 63,342,397 (GRCm39) R259G possibly damaging Het
Other mutations in Sdc3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00979:Sdc3 APN 4 130,545,991 (GRCm39) missense unknown
IGL01715:Sdc3 APN 4 130,546,378 (GRCm39) missense probably damaging 0.99
IGL02160:Sdc3 APN 4 130,545,886 (GRCm39) splice site probably benign
IGL03134:Sdc3 UTSW 4 130,548,815 (GRCm39) missense probably benign 0.00
R2426:Sdc3 UTSW 4 130,546,114 (GRCm39) missense unknown
R4678:Sdc3 UTSW 4 130,545,907 (GRCm39) utr 5 prime probably benign
R4786:Sdc3 UTSW 4 130,550,079 (GRCm39) missense probably damaging 0.97
R5182:Sdc3 UTSW 4 130,548,995 (GRCm39) unclassified probably benign
R5225:Sdc3 UTSW 4 130,546,087 (GRCm39) missense unknown
R6111:Sdc3 UTSW 4 130,546,153 (GRCm39) missense unknown
R6980:Sdc3 UTSW 4 130,544,233 (GRCm39) utr 5 prime probably benign
R7881:Sdc3 UTSW 4 130,544,244 (GRCm39) missense unknown
R7920:Sdc3 UTSW 4 130,546,507 (GRCm39) missense probably benign 0.00
R8514:Sdc3 UTSW 4 130,546,072 (GRCm39) missense unknown
R8815:Sdc3 UTSW 4 130,546,336 (GRCm39) missense probably benign 0.18
R8909:Sdc3 UTSW 4 130,546,094 (GRCm39) missense unknown
R9116:Sdc3 UTSW 4 130,546,352 (GRCm39) missense probably benign 0.33
R9251:Sdc3 UTSW 4 130,548,513 (GRCm39) unclassified probably benign
R9764:Sdc3 UTSW 4 130,546,048 (GRCm39) missense unknown
Predicted Primers PCR Primer
(F):5'- AACTATGGCCACAGCACCTG -3'
(R):5'- TAACAGCCTTTACTCAGCTGG -3'

Sequencing Primer
(F):5'- GCCACCACTGCCCCTAG -3'
(R):5'- TTACTCAGCTGGCCTGGC -3'
Posted On 2015-12-29