Incidental Mutation 'IGL02456:Kdm5c'
ID 294162
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Kdm5c
Ensembl Gene ENSMUSG00000025332
Gene Name lysine demethylase 5C
Synonyms D930009K15Rik, Jarid1c, Smcx
Accession Numbers
Essential gene? Not available question?
Stock # IGL02456
Quality Score
Status
Chromosome X
Chromosomal Location 151016016-151057531 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 151029314 bp (GRCm39)
Zygosity Heterozygous
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]
AlphaFold P41230
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
4921511C20Rik T A X: 126,302,584 (GRCm39) Y174* probably null Het
Apc C A 18: 34,446,935 (GRCm39) S1243* probably null Het
Atp8b5 A G 4: 43,365,578 (GRCm39) T731A probably benign Het
Bcl2a1c T A 9: 114,159,458 (GRCm39) F79I probably damaging Het
Brip1 G T 11: 85,955,925 (GRCm39) L863I possibly damaging Het
Cbx4 T A 11: 118,972,938 (GRCm39) K146* probably null Het
Ces1a C T 8: 93,766,126 (GRCm39) V163I possibly damaging Het
Ces5a C T 8: 94,255,272 (GRCm39) probably benign Het
Cfhr1 A C 1: 139,484,131 (GRCm39) N128K possibly damaging Het
Clcn3 T C 8: 61,394,391 (GRCm39) D46G probably damaging Het
Cntnap1 T G 11: 101,068,955 (GRCm39) I166S probably benign Het
Cntnap3 A T 13: 64,946,872 (GRCm39) probably benign Het
Cntnap5c T A 17: 58,714,739 (GRCm39) probably benign Het
Ddx23 A T 15: 98,545,430 (GRCm39) V626E probably damaging Het
Dele1 T A 18: 38,394,177 (GRCm39) L458Q probably damaging Het
Gcm2 T C 13: 41,256,477 (GRCm39) Y424C probably benign Het
Gm9964 A G 11: 79,187,196 (GRCm39) F84L probably damaging Het
Grn T A 11: 102,326,930 (GRCm39) D509E probably benign Het
Iho1 G T 9: 108,283,820 (GRCm39) T208K probably benign Het
Ly75 C T 2: 60,124,125 (GRCm39) M1717I probably benign Het
Map1a C A 2: 121,129,134 (GRCm39) P133T probably damaging Het
Mpp2 C A 11: 101,950,199 (GRCm39) A552S possibly damaging Het
Mtr T C 13: 12,213,980 (GRCm39) I897M probably damaging Het
Npas3 A T 12: 54,095,550 (GRCm39) I337F probably damaging Het
Nup85 T C 11: 115,472,691 (GRCm39) probably benign Het
Or10a49 A G 7: 108,468,257 (GRCm39) Y35H probably benign Het
Or10al2 T A 17: 37,983,340 (GRCm39) M142K possibly damaging Het
Or2t46 T A 11: 58,472,024 (GRCm39) L118H possibly damaging Het
Or51l4 T A 7: 103,404,700 (GRCm39) I31F possibly damaging Het
Or56a5 T C 7: 104,792,966 (GRCm39) N178S probably damaging Het
Pdia4 A T 6: 47,780,429 (GRCm39) D301E probably benign Het
Phf2 C A 13: 48,982,322 (GRCm39) G134C unknown Het
Polr2h T A 16: 20,539,352 (GRCm39) L76H probably damaging Het
Rbm47 G A 5: 66,184,364 (GRCm39) R80C probably damaging Het
Sfmbt1 T C 14: 30,507,837 (GRCm39) S286P probably damaging Het
Slc5a12 T C 2: 110,447,179 (GRCm39) probably benign Het
Tacc2 T C 7: 130,227,991 (GRCm39) S1559P probably benign Het
Tbc1d16 T G 11: 119,101,372 (GRCm39) H46P probably damaging Het
Tbck A G 3: 132,440,475 (GRCm39) probably benign Het
Tmtc4 A T 14: 123,163,374 (GRCm39) probably null Het
Ttc13 T C 8: 125,417,100 (GRCm39) probably null Het
Ttc17 T C 2: 94,193,130 (GRCm39) probably benign Het
Vmn1r121 T A 7: 20,832,438 (GRCm39) M1L possibly damaging Het
Vps13c T C 9: 67,860,258 (GRCm39) S2825P probably damaging Het
Zan A C 5: 137,445,106 (GRCm39) S1718A unknown Het
Zfp39 G T 11: 58,793,626 (GRCm39) Y37* probably null Het
Zfp407 T C 18: 84,576,766 (GRCm39) N1449S probably damaging Het
Zhx2 C A 15: 57,687,035 (GRCm39) D801E possibly damaging Het
Other mutations in Kdm5c
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02103:Kdm5c APN X 151,031,762 (GRCm39) missense probably damaging 0.96
IGL02434:Kdm5c APN X 151,016,558 (GRCm39) start codon destroyed probably null 0.87
Posted On 2015-04-16