Incidental Mutation 'IGL02434:Kdm5c'
ID293226
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 #IGL02434
Quality Score
Status
ChromosomeX
Chromosomal Location152233020-152274535 bp(+) (GRCm38)
Type of Mutationstart codon destroyed
DNA Base Change (assembly) T to A at 152233562 bp
ZygosityHeterozygous
Amino Acid Change Methionine to Lysine at position 1 (M1K)
Ref Sequence ENSEMBL: ENSMUSP00000108207 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000082177] [ENSMUST00000112584] [ENSMUST00000112588]
Predicted Effect probably null
Transcript: ENSMUST00000082177
AA Change: M1K

PolyPhen 2 Score 0.865 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000080814
Gene: ENSMUSG00000025332
AA Change: M1K

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 null
Transcript: ENSMUST00000112584
AA Change: M1K

PolyPhen 2 Score 0.865 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000108203
Gene: ENSMUSG00000025332
AA Change: M1K

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 null
Transcript: ENSMUST00000112588
AA Change: M1K

PolyPhen 2 Score 0.865 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000108207
Gene: ENSMUSG00000025332
AA Change: M1K

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: 37 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ago2 C A 15: 73,121,081 G525V probably damaging Het
Agxt2 T C 15: 10,358,600 S2P possibly damaging Het
Atg2b C T 12: 105,639,207 V339I probably benign Het
Btc T A 5: 91,362,327 I136F probably damaging Het
Cemip A T 7: 83,955,284 M850K probably damaging Het
Cfap54 T A 10: 93,066,754 T179S probably benign Het
Chd7 T C 4: 8,752,145 L214P probably benign Het
Garnl3 T A 2: 33,054,205 N114I probably damaging Het
Gm10010 G T 6: 128,200,470 noncoding transcript Het
Gstcd A G 3: 132,996,202 probably benign Het
Htr2b A G 1: 86,110,770 V38A probably benign Het
Hyal4 G A 6: 24,763,858 W339* probably null Het
Ifnb1 A G 4: 88,522,518 V86A probably damaging Het
Itpr1 A G 6: 108,489,922 probably null Het
Jag1 T C 2: 137,087,155 S794G probably benign Het
Lct A G 1: 128,303,790 V774A probably damaging Het
Man2a2 G A 7: 80,359,640 A822V probably damaging Het
Med14 A T X: 12,745,824 D371E possibly damaging Het
Nrcam A G 12: 44,590,243 probably benign Het
Olfr116 T A 17: 37,624,576 N20Y possibly damaging Het
Olfr670 A T 7: 104,960,072 M220K probably benign Het
Olfr670 A T 7: 104,960,074 Y219* probably null Het
Pitpnm1 C T 19: 4,103,377 R178W probably benign Het
Prkcg A G 7: 3,318,890 I324V probably benign Het
Prpmp5 T A 6: 132,312,376 R162W unknown Het
Prr30 A T 14: 101,198,368 C253S possibly damaging Het
Ptgis A T 2: 167,240,342 probably null Het
Rab11fip3 C T 17: 26,068,835 A115T possibly damaging Het
Reps2 C T X: 162,526,257 probably null Het
Rev3l A G 10: 39,822,591 D1028G probably damaging Het
Rsbn1l T C 5: 20,919,734 R357G probably damaging Het
Scn5a A G 9: 119,533,793 L587P possibly damaging Het
Tanc2 C T 11: 105,780,042 T155I probably benign Het
Tfb2m A G 1: 179,532,135 probably benign Het
Tfpi A G 2: 84,452,548 probably benign Het
Tg T C 15: 66,764,342 S593P probably damaging Het
Unc13c T C 9: 73,932,628 S314G probably benign Het
Other mutations in Kdm5c
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02103:Kdm5c APN X 152248766 missense probably damaging 0.96
IGL02456:Kdm5c APN X 152246318 missense probably damaging 1.00
Posted On2015-04-16