Incidental Mutation 'IGL02456:Kdm5c'
ID294162
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Kdm5c
Ensembl Gene ENSMUSG00000025332
Gene Namelysine (K)-specific demethylase 5C
SynonymsJarid1c, D930009K15Rik, Smcx
Accession Numbers
Is this an essential gene? Not available question?
Stock #IGL02456
Quality Score
Status
ChromosomeX
Chromosomal Location152233020-152274535 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) G to A at 152246318 bp
ZygosityHeterozygous
Amino Acid Change Aspartic acid to Asparagine at position 343 (D343N)
Ref Sequence ENSEMBL: ENSMUSP00000108207 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000082177] [ENSMUST00000112584] [ENSMUST00000112588]
Predicted Effect probably damaging
Transcript: ENSMUST00000082177
AA Change: D302N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000080814
Gene: ENSMUSG00000025332
AA Change: D302N

DomainStartEndE-ValueType
JmjN 13 54 3.45e-23 SMART
ARID 21 124 1.6e-9 SMART
PHD 285 331 4.28e-13 SMART
JmjC 427 593 6.31e-64 SMART
Pfam:zf-C5HC2 666 719 2.8e-19 PFAM
Pfam:PLU-1 730 1059 6.6e-102 PFAM
low complexity region 1134 1145 N/A INTRINSIC
PHD 1146 1207 6.01e-8 SMART
low complexity region 1349 1360 N/A INTRINSIC
low complexity region 1397 1417 N/A INTRINSIC
low complexity region 1436 1462 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000112584
AA Change: D343N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000108203
Gene: ENSMUSG00000025332
AA Change: D343N

DomainStartEndE-ValueType
JmjN 13 54 3.45e-23 SMART
ARID 76 165 1.09e-34 SMART
BRIGHT 80 170 1.3e-34 SMART
PHD 326 372 4.28e-13 SMART
JmjC 468 634 6.31e-64 SMART
Pfam:zf-C5HC2 707 759 2.4e-18 PFAM
Pfam:PLU-1 772 1100 9.3e-91 PFAM
low complexity region 1175 1186 N/A INTRINSIC
PHD 1187 1248 6.01e-8 SMART
low complexity region 1393 1404 N/A INTRINSIC
low complexity region 1441 1461 N/A INTRINSIC
low complexity region 1480 1506 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000112588
AA Change: D343N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000108207
Gene: ENSMUSG00000025332
AA Change: D343N

DomainStartEndE-ValueType
JmjN 13 54 3.45e-23 SMART
ARID 76 165 1.09e-34 SMART
BRIGHT 80 170 1.3e-34 SMART
PHD 326 372 4.28e-13 SMART
JmjC 468 634 6.31e-64 SMART
Pfam:zf-C5HC2 707 760 2.9e-19 PFAM
Pfam:PLU-1 771 1100 6.9e-102 PFAM
low complexity region 1175 1186 N/A INTRINSIC
PHD 1187 1248 6.01e-8 SMART
low complexity region 1390 1401 N/A INTRINSIC
low complexity region 1438 1458 N/A INTRINSIC
low complexity region 1477 1503 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154938
Coding Region Coverage
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the SMCY homolog family and encodes a protein with one ARID domain, one JmjC domain, one JmjN domain and two PHD-type zinc fingers. The DNA-binding motifs suggest this protein is involved in the regulation of transcription and chromatin remodeling. Mutations in this gene have been associated with X-linked mental retardation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
PHENOTYPE: Male chimeras hemizygous for a gene trapped allele exhibit posterior patterning defects and abnormal heart morphology at E9.5. Chimeras hemizygous for a different gene trapped allele appear normal at E10.5. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 48 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
0610009O20Rik T A 18: 38,261,124 L458Q probably damaging Het
4921511C20Rik T A X: 127,394,961 Y174* probably null Het
Apc C A 18: 34,313,882 S1243* probably null Het
Atp8b5 A G 4: 43,365,578 T731A probably benign Het
Bcl2a1c T A 9: 114,330,390 F79I probably damaging Het
Brip1 G T 11: 86,065,099 L863I possibly damaging Het
Cbx4 T A 11: 119,082,112 K146* probably null Het
Ccdc36 G T 9: 108,406,621 T208K probably benign Het
Ces1a C T 8: 93,039,498 V163I possibly damaging Het
Ces5a C T 8: 93,528,644 probably benign Het
Cfhr1 A C 1: 139,556,393 N128K possibly damaging Het
Clcn3 T C 8: 60,941,357 D46G probably damaging Het
Cntnap1 T G 11: 101,178,129 I166S probably benign Het
Cntnap3 A T 13: 64,799,058 probably benign Het
Cntnap5c T A 17: 58,407,744 probably benign Het
Ddx23 A T 15: 98,647,549 V626E probably damaging Het
Gcm2 T C 13: 41,103,001 Y424C probably benign Het
Gm9964 A G 11: 79,296,370 F84L probably damaging Het
Grn T A 11: 102,436,104 D509E probably benign Het
Ly75 C T 2: 60,293,781 M1717I probably benign Het
Map1a C A 2: 121,298,653 P133T probably damaging Het
Mpp2 C A 11: 102,059,373 A552S possibly damaging Het
Mtr T C 13: 12,199,094 I897M probably damaging Het
Npas3 A T 12: 54,048,767 I337F probably damaging Het
Nup85 T C 11: 115,581,865 probably benign Het
Olfr118 T A 17: 37,672,449 M142K possibly damaging Het
Olfr325 T A 11: 58,581,198 L118H possibly damaging Het
Olfr517 A G 7: 108,869,050 Y35H probably benign Het
Olfr630 T A 7: 103,755,493 I31F possibly damaging Het
Olfr683 T C 7: 105,143,759 N178S probably damaging Het
Pdia4 A T 6: 47,803,495 D301E probably benign Het
Phf2 C A 13: 48,828,846 G134C unknown Het
Polr2h T A 16: 20,720,602 L76H probably damaging Het
Rbm47 G A 5: 66,027,021 R80C probably damaging Het
Sfmbt1 T C 14: 30,785,880 S286P probably damaging Het
Slc5a12 T C 2: 110,616,834 probably benign Het
Tacc2 T C 7: 130,626,261 S1559P probably benign Het
Tbc1d16 T G 11: 119,210,546 H46P probably damaging Het
Tbck A G 3: 132,734,714 probably benign Het
Tmtc4 A T 14: 122,925,962 probably null Het
Ttc13 T C 8: 124,690,361 probably null Het
Ttc17 T C 2: 94,362,785 probably benign Het
Vmn1r121 T A 7: 21,098,513 M1L possibly damaging Het
Vps13c T C 9: 67,952,976 S2825P probably damaging Het
Zan A C 5: 137,446,844 S1718A unknown Het
Zfp39 G T 11: 58,902,800 Y37* probably null Het
Zfp407 T C 18: 84,558,641 N1449S probably damaging Het
Zhx2 C A 15: 57,823,639 D801E possibly damaging Het
Other mutations in Kdm5c
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02103:Kdm5c APN X 152248766 missense probably damaging 0.96
IGL02434:Kdm5c APN X 152233562 start codon destroyed probably null 0.87
Posted On2015-04-16