Incidental Mutation 'R5374:Kdm5d'
ID 428982
Institutional Source Beutler Lab
Gene Symbol Kdm5d
Ensembl Gene ENSMUSG00000056673
Gene Name lysine demethylase 5D
Synonyms Smcy, HY, Jarid1d
MMRRC Submission 042950-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.071) question?
Stock # R5374 (G1)
Quality Score 222
Status Validated
Chromosome Y
Chromosomal Location 897566-943813 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 927995 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Serine at position 756 (P756S)
Ref Sequence ENSEMBL: ENSMUSP00000061095 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000055032] [ENSMUST00000186696] [ENSMUST00000186726]
AlphaFold Q62240
Predicted Effect probably benign
Transcript: ENSMUST00000055032
AA Change: P756S

PolyPhen 2 Score 0.089 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: P756S

DomainStartEndE-ValueType
JmjN 13 54 3.45e-23 SMART
ARID 76 165 4.84e-36 SMART
BRIGHT 80 170 4.48e-38 SMART
PHD 325 371 8.56e-13 SMART
JmjC 467 633 2.52e-63 SMART
Pfam:zf-C5HC2 706 758 5.2e-18 PFAM
Pfam:PLU-1 771 1096 1.4e-89 PFAM
low complexity region 1147 1156 N/A INTRINSIC
low complexity region 1164 1181 N/A INTRINSIC
PHD 1182 1243 2.54e-6 SMART
coiled coil region 1290 1318 N/A INTRINSIC
low complexity region 1340 1351 N/A INTRINSIC
low complexity region 1395 1406 N/A INTRINSIC
low complexity region 1453 1459 N/A INTRINSIC
low complexity region 1525 1541 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000186696
SMART Domains Protein: ENSMUSP00000140663
Gene: ENSMUSG00000056673

DomainStartEndE-ValueType
JmjN 13 54 3.45e-23 SMART
ARID 76 165 4.84e-36 SMART
BRIGHT 80 170 4.48e-38 SMART
PHD 325 371 8.56e-13 SMART
JmjC 467 633 2.52e-63 SMART
low complexity region 675 689 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000186726
SMART Domains Protein: ENSMUSP00000140462
Gene: ENSMUSG00000056673

DomainStartEndE-ValueType
JmjN 13 54 1.4e-25 SMART
ARID 76 165 3.8e-40 SMART
BRIGHT 80 170 2.3e-40 SMART
Blast:ARID 175 260 1e-41 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000187296
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.2%
Validation Efficiency 96% (81/84)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein containing zinc finger domains. A short peptide derived from this protein is a minor histocompatibility antigen which can lead to graft rejection of male donor cells in a female recipient. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
Allele List at MGI
Other mutations in this stock
Total: 77 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik A G 3: 137,773,396 (GRCm39) S862G probably benign Het
Adgrf1 G A 17: 43,601,896 (GRCm39) probably benign Het
Adss2 T G 1: 177,623,954 (GRCm39) I3L probably benign Het
Anapc7 T A 5: 122,576,280 (GRCm39) D302E probably benign Het
Ank3 A G 10: 69,789,306 (GRCm39) probably null Het
Astn2 A C 4: 65,315,242 (GRCm39) V1145G probably damaging Het
Babam2 C T 5: 32,164,574 (GRCm39) probably benign Het
Blvrb A G 7: 27,165,271 (GRCm39) H238R possibly damaging Het
Cacna1b C T 2: 24,596,228 (GRCm39) V488I probably damaging Het
Ccdc88a C T 11: 29,413,409 (GRCm39) T649M possibly damaging Het
Cdh12 A C 15: 21,583,998 (GRCm39) S613R probably damaging Het
Cisd2 A G 3: 135,114,596 (GRCm39) V125A probably benign Het
Clcn2 C A 16: 20,528,419 (GRCm39) G478W possibly damaging Het
Cntnap2 T A 6: 47,084,903 (GRCm39) H1121Q probably benign Het
Corin A T 5: 72,462,296 (GRCm39) C876S probably damaging Het
Cox7c T C 13: 86,194,739 (GRCm39) Y19C probably benign Het
Cplane1 T C 15: 8,300,287 (GRCm39) V3198A unknown Het
Cspp1 T G 1: 10,204,351 (GRCm39) L1038R probably damaging Het
Cwc15 A G 9: 14,416,234 (GRCm39) K147E possibly damaging Het
Dlgap2 A G 8: 14,873,614 (GRCm39) D739G probably benign Het
Dmxl2 A G 9: 54,276,473 (GRCm39) probably benign Het
Dock5 A G 14: 68,043,205 (GRCm39) V864A possibly damaging Het
Dock7 A G 4: 98,877,275 (GRCm39) F1088L possibly damaging Het
Dpysl3 T C 18: 43,494,101 (GRCm39) Y193C probably damaging Het
Dtna T C 18: 23,784,670 (GRCm39) Y730H probably damaging Het
Dusp3 A G 11: 101,875,451 (GRCm39) Y38H possibly damaging Het
Eif3m A T 2: 104,843,277 (GRCm39) I151N probably damaging Het
Entpd2 C T 2: 25,289,738 (GRCm39) T380I probably damaging Het
Epb41l3 C A 17: 69,593,795 (GRCm39) H810N probably damaging Het
Fcrl5 A G 3: 87,353,698 (GRCm39) T348A probably benign Het
Ginm1 A G 10: 7,655,078 (GRCm39) S55P probably damaging Het
Glt1d1 C A 5: 127,734,148 (GRCm39) probably null Het
Gm15433 T A 1: 84,941,833 (GRCm39) noncoding transcript Het
Gm8221 A G 15: 77,510,352 (GRCm39) noncoding transcript Het
Gramd1c A G 16: 43,803,604 (GRCm39) V603A probably benign Het
Grm1 A G 10: 10,956,186 (GRCm39) S33P probably benign Het
Gstp3 T C 19: 4,107,922 (GRCm39) N137S possibly damaging Het
Ly75 A T 2: 60,142,115 (GRCm39) L1332M possibly damaging Het
Med1 T A 11: 98,054,789 (GRCm39) K378N probably damaging Het
Mn1 A G 5: 111,569,752 (GRCm39) probably null Het
Mpo T C 11: 87,694,437 (GRCm39) probably null Het
Nom1 C G 5: 29,646,377 (GRCm39) R555G probably damaging Het
Nsmce4a C T 7: 130,139,900 (GRCm39) R276Q probably benign Het
Nt5c G A 11: 115,381,643 (GRCm39) probably null Het
Olfr908 CACAACAACA CACAACA 9: 38,427,434 (GRCm39) probably benign Het
Or52e18 G T 7: 104,609,203 (GRCm39) H245Q probably damaging Het
Or5p52 T C 7: 107,502,698 (GRCm39) I258T possibly damaging Het
Pcdhga4 T C 18: 37,818,649 (GRCm39) V66A probably damaging Het
Pik3c3 T C 18: 30,445,614 (GRCm39) S534P probably benign Het
Pla2g4e A T 2: 120,016,876 (GRCm39) C222S probably benign Het
Plch1 A C 3: 63,605,499 (GRCm39) H1468Q probably benign Het
Psd2 T A 18: 36,140,556 (GRCm39) W610R probably damaging Het
Ptgs1 A T 2: 36,141,198 (GRCm39) K548N probably damaging Het
Ptprz1 T A 6: 23,007,354 (GRCm39) V1639E probably damaging Het
Rangap1 A T 15: 81,590,695 (GRCm39) S466T probably benign Het
Rgsl1 C T 1: 153,666,053 (GRCm39) V986I probably benign Het
Rhobtb3 T C 13: 76,027,014 (GRCm39) Y453C probably damaging Het
Rspry1 T C 8: 95,349,636 (GRCm39) V8A probably benign Het
Rspry1 C A 8: 95,380,892 (GRCm39) R399S probably benign Het
Rufy4 T C 1: 74,186,822 (GRCm39) C537R probably damaging Het
Rxfp2 A G 5: 149,993,725 (GRCm39) T596A probably benign Het
Sap18b G A 8: 96,551,998 (GRCm39) A3T unknown Het
Serpina3j A G 12: 104,280,986 (GRCm39) D53G probably damaging Het
Skint3 T A 4: 112,155,386 (GRCm39) D381E possibly damaging Het
Slirp T C 12: 87,496,192 (GRCm39) S96P possibly damaging Het
Snx6 T C 12: 54,817,513 (GRCm39) E128G probably damaging Het
Stap1 A G 5: 86,238,787 (GRCm39) T152A possibly damaging Het
Tcf20 A T 15: 82,736,158 (GRCm39) N1764K probably damaging Het
Thap2 A T 10: 115,208,744 (GRCm39) Y125* probably null Het
Ticrr T G 7: 79,340,690 (GRCm39) Y1031* probably null Het
Tnrc18 G A 5: 142,725,911 (GRCm39) R1793C unknown Het
Trpm3 C T 19: 22,903,548 (GRCm39) R945* probably null Het
Ugt1a10 T A 1: 87,983,632 (GRCm39) D143E probably damaging Het
Ush2a C T 1: 188,487,403 (GRCm39) T3057M probably benign Het
Zc3h6 A T 2: 128,844,076 (GRCm39) I207F possibly damaging Het
Zfp518a T C 19: 40,901,954 (GRCm39) S628P probably benign Het
Zup1 T C 10: 33,803,462 (GRCm39) N541D possibly damaging Het
Other mutations in Kdm5d
AlleleSourceChrCoordTypePredicted EffectPPH Score
R0013:Kdm5d UTSW Y 941,715 (GRCm39) missense probably benign 0.37
R0013:Kdm5d UTSW Y 941,715 (GRCm39) missense probably benign 0.37
R0426:Kdm5d UTSW Y 942,437 (GRCm39) splice site probably benign
R0486:Kdm5d UTSW Y 927,107 (GRCm39) missense probably damaging 1.00
R0620:Kdm5d UTSW Y 927,330 (GRCm39) missense probably damaging 0.98
R0781:Kdm5d UTSW Y 910,539 (GRCm39) missense probably damaging 1.00
R1015:Kdm5d UTSW Y 941,687 (GRCm39) missense possibly damaging 0.95
R1110:Kdm5d UTSW Y 910,539 (GRCm39) missense probably damaging 1.00
R1163:Kdm5d UTSW Y 898,029 (GRCm39) missense probably benign 0.18
R1203:Kdm5d UTSW Y 941,011 (GRCm39) missense probably damaging 1.00
R1238:Kdm5d UTSW Y 941,282 (GRCm39) missense probably damaging 1.00
R1723:Kdm5d UTSW Y 927,753 (GRCm39) missense probably damaging 1.00
R1842:Kdm5d UTSW Y 927,798 (GRCm39) missense probably damaging 1.00
R1885:Kdm5d UTSW Y 940,781 (GRCm39) splice site probably null
R2131:Kdm5d UTSW Y 941,483 (GRCm39) missense probably benign 0.02
R2571:Kdm5d UTSW Y 940,932 (GRCm39) missense probably benign 0.11
R2931:Kdm5d UTSW Y 942,992 (GRCm39) missense probably benign 0.18
R3123:Kdm5d UTSW Y 900,558 (GRCm39) missense possibly damaging 0.63
R3919:Kdm5d UTSW Y 939,914 (GRCm39) missense probably damaging 1.00
R4018:Kdm5d UTSW Y 910,441 (GRCm39) splice site probably benign
R4031:Kdm5d UTSW Y 916,910 (GRCm39) missense probably damaging 1.00
R4403:Kdm5d UTSW Y 899,830 (GRCm39) missense probably damaging 1.00
R4571:Kdm5d UTSW Y 927,110 (GRCm39) missense probably damaging 1.00
R4583:Kdm5d UTSW Y 914,134 (GRCm39) missense probably damaging 1.00
R4962:Kdm5d UTSW Y 940,624 (GRCm39) missense probably damaging 1.00
R5105:Kdm5d UTSW Y 941,752 (GRCm39) missense probably benign 0.00
R5249:Kdm5d UTSW Y 916,692 (GRCm39) missense probably damaging 1.00
R5367:Kdm5d UTSW Y 941,645 (GRCm39) missense probably benign 0.05
R5373:Kdm5d UTSW Y 927,995 (GRCm39) missense probably benign 0.09
R5876:Kdm5d UTSW Y 900,525 (GRCm39) missense probably damaging 1.00
R5909:Kdm5d UTSW Y 941,306 (GRCm39) missense probably benign 0.01
R6014:Kdm5d UTSW Y 921,528 (GRCm39) missense probably benign 0.45
R6109:Kdm5d UTSW Y 921,501 (GRCm39) missense probably damaging 1.00
R6251:Kdm5d UTSW Y 921,693 (GRCm39) missense probably damaging 1.00
R6349:Kdm5d UTSW Y 916,847 (GRCm39) missense probably damaging 0.99
R6450:Kdm5d UTSW Y 927,056 (GRCm39) missense probably damaging 1.00
R6595:Kdm5d UTSW Y 939,829 (GRCm39) missense probably benign
R6628:Kdm5d UTSW Y 900,525 (GRCm39) missense probably damaging 1.00
R6745:Kdm5d UTSW Y 927,112 (GRCm39) missense probably benign 0.28
R6867:Kdm5d UTSW Y 927,425 (GRCm39) missense probably benign
R6963:Kdm5d UTSW Y 937,975 (GRCm39) missense probably benign 0.01
R7163:Kdm5d UTSW Y 899,940 (GRCm39) missense probably damaging 1.00
R7374:Kdm5d UTSW Y 941,491 (GRCm39) missense probably benign 0.41
R7483:Kdm5d UTSW Y 914,044 (GRCm39) missense possibly damaging 0.50
R7501:Kdm5d UTSW Y 941,488 (GRCm39) missense probably damaging 1.00
R7815:Kdm5d UTSW Y 940,702 (GRCm39) missense probably damaging 1.00
R7835:Kdm5d UTSW Y 900,558 (GRCm39) missense possibly damaging 0.63
R8057:Kdm5d UTSW Y 927,355 (GRCm39) missense possibly damaging 0.48
R8080:Kdm5d UTSW Y 910,742 (GRCm39) missense probably benign 0.01
R8130:Kdm5d UTSW Y 940,658 (GRCm39) missense possibly damaging 0.75
R8213:Kdm5d UTSW Y 941,515 (GRCm39) missense probably damaging 1.00
R8261:Kdm5d UTSW Y 936,929 (GRCm39) missense probably damaging 0.99
R8344:Kdm5d UTSW Y 942,477 (GRCm39) missense probably benign 0.05
R8348:Kdm5d UTSW Y 914,056 (GRCm39) missense probably benign 0.00
R8445:Kdm5d UTSW Y 916,874 (GRCm39) missense probably damaging 1.00
R8448:Kdm5d UTSW Y 914,056 (GRCm39) missense probably benign 0.00
R8754:Kdm5d UTSW Y 941,594 (GRCm39) missense probably damaging 1.00
R9203:Kdm5d UTSW Y 940,981 (GRCm39) missense probably damaging 0.99
R9259:Kdm5d UTSW Y 942,640 (GRCm39) missense possibly damaging 0.84
R9541:Kdm5d UTSW Y 910,801 (GRCm39) missense probably damaging 1.00
R9668:Kdm5d UTSW Y 943,075 (GRCm39) missense possibly damaging 0.73
Predicted Primers PCR Primer
(F):5'- GGCCTGTTATGACTGTCCAG -3'
(R):5'- GTTCCAATAGAGTGTTACCAGAAG -3'

Sequencing Primer
(F):5'- GCCTGTTATGACTGTCCAGATAGTC -3'
(R):5'- CTGATCATAGCTTAAAGGTTCTT -3'
Posted On 2016-09-06