Incidental Mutation 'IGL02103:Kdm5c'
ID279836
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 #IGL02103
Quality Score
Status
ChromosomeX
Chromosomal Location152233020-152274535 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to A at 152248766 bp
ZygosityHeterozygous
Amino Acid Change Phenylalanine to Leucine at position 408 (F408L)
Ref Sequence ENSEMBL: ENSMUSP00000080814 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000082177] [ENSMUST00000112584] [ENSMUST00000112588]
Predicted Effect probably damaging
Transcript: ENSMUST00000082177
AA Change: F408L

PolyPhen 2 Score 0.964 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000080814
Gene: ENSMUSG00000025332
AA Change: F408L

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 possibly damaging
Transcript: ENSMUST00000112584
AA Change: F449L

PolyPhen 2 Score 0.898 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000108203
Gene: ENSMUSG00000025332
AA Change: F449L

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 possibly damaging
Transcript: ENSMUST00000112588
AA Change: F449L

PolyPhen 2 Score 0.898 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000108207
Gene: ENSMUSG00000025332
AA Change: F449L

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: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcd4 G A 12: 84,612,364 T206M probably benign Het
Adcy3 T A 12: 4,134,390 V22D possibly damaging Het
Alb G A 5: 90,464,131 E140K probably benign Het
Aph1a G A 3: 95,895,813 V193I probably damaging Het
Asb2 G A 12: 103,333,496 R178* probably null Het
Celf3 A T 3: 94,486,801 Q137L probably damaging Het
Cmya5 T C 13: 93,092,127 D2151G probably benign Het
Cuedc1 T A 11: 88,188,799 S353T probably damaging Het
Dlg5 A C 14: 24,144,346 L1709R probably damaging Het
Dst T C 1: 34,190,118 I1939T possibly damaging Het
Emx2 A T 19: 59,461,698 N149I probably benign Het
Fancm A G 12: 65,095,784 D472G probably benign Het
Fasn T C 11: 120,811,936 Y1700C probably damaging Het
Fat2 T A 11: 55,289,296 R1406S probably damaging Het
Fat4 C A 3: 38,889,199 T747K probably damaging Het
Fer A G 17: 64,138,928 M795V probably benign Het
Gm5916 A G 9: 36,128,674 L6P probably damaging Het
Gpr139 A G 7: 119,145,132 F77L possibly damaging Het
Kcnu1 T C 8: 25,905,948 S654P possibly damaging Het
Kel A G 6: 41,702,389 S147P probably benign Het
Klra5 A T 6: 129,911,344 probably null Het
Mastl A G 2: 23,139,998 S239P probably benign Het
Med18 A T 4: 132,459,666 V174D probably damaging Het
Mgat4a A T 1: 37,462,926 M247K possibly damaging Het
Mx2 A C 16: 97,544,595 D71A probably damaging Het
Nxt1 G T 2: 148,675,644 E102* probably null Het
Olfr125 A G 17: 37,835,278 Q93R possibly damaging Het
Olfr410 A G 11: 74,335,036 F65S probably damaging Het
Olfr828 T C 9: 18,815,709 N195S probably damaging Het
Pcdhb16 T A 18: 37,480,108 V707E probably benign Het
Pdzrn4 T A 15: 92,769,887 V640E probably damaging Het
Piwil4 T C 9: 14,725,986 probably null Het
Pla2g4a A T 1: 149,901,199 D55E probably damaging Het
Plekhg2 C A 7: 28,360,076 R1276L probably damaging Het
Psd4 G A 2: 24,400,528 W539* probably null Het
Rae1 G A 2: 173,003,513 E33K probably damaging Het
Rbm12b1 T A 4: 12,145,563 F512I probably damaging Het
Rfx6 A G 10: 51,726,856 D823G possibly damaging Het
Samt3 A T X: 86,047,153 Q217L probably damaging Het
Selenbp2 A G 3: 94,698,131 N134S probably null Het
Selenoo T C 15: 89,099,970 V663A probably damaging Het
Sp4 G T 12: 118,299,549 T254N probably damaging Het
Spdya A G 17: 71,578,247 K232R probably benign Het
Stom A T 2: 35,320,389 V201E probably benign Het
Sycp3 A G 10: 88,466,472 K108R possibly damaging Het
Usp2 A G 9: 44,089,128 probably benign Het
Vmn1r226 T C 17: 20,687,664 S53P probably damaging Het
Vmn2r14 C T 5: 109,224,483 G47D probably damaging Het
Vwf T G 6: 125,646,355 L1805W probably damaging Het
Washc3 A T 10: 88,201,825 Q22L probably damaging Het
Wdr81 T A 11: 75,444,720 D1761V probably damaging Het
Other mutations in Kdm5c
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02434:Kdm5c APN X 152233562 start codon destroyed probably null 0.87
IGL02456:Kdm5c APN X 152246318 missense probably damaging 1.00
Posted On2015-04-16