Incidental Mutation 'IGL02434:Kdm5c'
ID 293226
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 # IGL02434
Quality Score
Status
Chromosome X
Chromosomal Location 151016016-151057531 bp(+) (GRCm39)
Type of Mutation start codon destroyed
DNA Base Change (assembly) T to A at 151016558 bp (GRCm39)
Zygosity Heterozygous
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]
AlphaFold P41230
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: 72,992,930 (GRCm39) G525V probably damaging Het
Agxt2 T C 15: 10,358,686 (GRCm39) S2P possibly damaging Het
Atg2b C T 12: 105,605,466 (GRCm39) V339I probably benign Het
Btc T A 5: 91,510,186 (GRCm39) I136F probably damaging Het
Cemip A T 7: 83,604,492 (GRCm39) M850K probably damaging Het
Cfap54 T A 10: 92,902,616 (GRCm39) T179S probably benign Het
Chd7 T C 4: 8,752,145 (GRCm39) L214P probably benign Het
Garnl3 T A 2: 32,944,217 (GRCm39) N114I probably damaging Het
Gm10010 G T 6: 128,177,433 (GRCm39) noncoding transcript Het
Gstcd A G 3: 132,701,963 (GRCm39) probably benign Het
Htr2b A G 1: 86,038,492 (GRCm39) V38A probably benign Het
Hyal4 G A 6: 24,763,857 (GRCm39) W339* probably null Het
Ifnb1 A G 4: 88,440,755 (GRCm39) V86A probably damaging Het
Itpr1 A G 6: 108,466,883 (GRCm39) probably null Het
Jag1 T C 2: 136,929,075 (GRCm39) S794G probably benign Het
Lct A G 1: 128,231,527 (GRCm39) V774A probably damaging Het
Man2a2 G A 7: 80,009,388 (GRCm39) A822V probably damaging Het
Med14 A T X: 12,612,063 (GRCm39) D371E possibly damaging Het
Nrcam A G 12: 44,637,026 (GRCm39) probably benign Het
Or14j10 T A 17: 37,935,467 (GRCm39) N20Y possibly damaging Het
Or52e18 A T 7: 104,609,279 (GRCm39) M220K probably benign Het
Or52e18 A T 7: 104,609,281 (GRCm39) Y219* probably null Het
Pitpnm1 C T 19: 4,153,377 (GRCm39) R178W probably benign Het
Prb1b T A 6: 132,289,339 (GRCm39) R162W unknown Het
Prkcg A G 7: 3,367,406 (GRCm39) I324V probably benign Het
Prr30 A T 14: 101,435,804 (GRCm39) C253S possibly damaging Het
Ptgis A T 2: 167,082,262 (GRCm39) probably null Het
Rab11fip3 C T 17: 26,287,809 (GRCm39) A115T possibly damaging Het
Reps2 C T X: 161,309,253 (GRCm39) probably null Het
Rev3l A G 10: 39,698,587 (GRCm39) D1028G probably damaging Het
Rsbn1l T C 5: 21,124,732 (GRCm39) R357G probably damaging Het
Scn5a A G 9: 119,362,859 (GRCm39) L587P possibly damaging Het
Tanc2 C T 11: 105,670,868 (GRCm39) T155I probably benign Het
Tfb2m A G 1: 179,359,700 (GRCm39) probably benign Het
Tfpi A G 2: 84,282,892 (GRCm39) probably benign Het
Tg T C 15: 66,636,191 (GRCm39) S593P probably damaging Het
Unc13c T C 9: 73,839,910 (GRCm39) S314G probably benign Het
Other mutations in Kdm5c
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02103:Kdm5c APN X 151,031,762 (GRCm39) missense probably damaging 0.96
IGL02456:Kdm5c APN X 151,029,314 (GRCm39) missense probably damaging 1.00
Posted On 2015-04-16