Incidental Mutation 'R9668:Kdm5d'
ID 727962
Institutional Source Beutler Lab
Gene Symbol Kdm5d
Ensembl Gene ENSMUSG00000056673
Gene Name lysine demethylase 5D
Synonyms Smcy, HY, Jarid1d
MMRRC Submission
Accession Numbers
Essential gene? Probably non essential (E-score: 0.071) question?
Stock # R9668 (G1)
Quality Score 221.999
Status Not validated
Chromosome Y
Chromosomal Location 897566-943813 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 943075 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Arginine at position 1519 (S1519R)
Ref Sequence ENSEMBL: ENSMUSP00000061095 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000055032] [ENSMUST00000186696] [ENSMUST00000186726]
AlphaFold Q62240
Predicted Effect possibly damaging
Transcript: ENSMUST00000055032
AA Change: S1519R

PolyPhen 2 Score 0.734 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: S1519R

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency
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: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acox1 G T 11: 116,089,137 (GRCm39) Y60* probably null Het
Acp7 T A 7: 28,314,562 (GRCm39) probably null Het
Adamts17 G A 7: 66,797,438 (GRCm39) V1052I possibly damaging Het
Ankrd13b T A 11: 77,368,594 (GRCm39) E42V possibly damaging Het
Ano1 C A 7: 144,164,579 (GRCm39) probably null Het
Atp5pb C T 3: 105,863,356 (GRCm39) V27I probably benign Het
C2cd2 A G 16: 97,671,418 (GRCm39) S494P probably damaging Het
Cd320 G A 17: 34,065,113 (GRCm39) C82Y probably damaging Het
Cdc16 T A 8: 13,817,552 (GRCm39) S288T possibly damaging Het
Chrne A G 11: 70,507,779 (GRCm39) probably null Het
Col12a1 G A 9: 79,546,960 (GRCm39) Q2291* probably null Het
Cps1 A G 1: 67,213,649 (GRCm39) S794G probably benign Het
Csmd1 A T 8: 16,261,772 (GRCm39) D908E probably benign Het
Dpf1 C T 7: 29,009,084 (GRCm39) Q70* probably null Het
Fam227a A T 15: 79,526,444 (GRCm39) N129K probably benign Het
Fcho2 T A 13: 98,913,965 (GRCm39) I211F probably benign Het
Fezf1 T C 6: 23,247,574 (GRCm39) D167G probably benign Het
Flt3 G A 5: 147,293,694 (GRCm39) P461S probably benign Het
Fry G T 5: 150,282,318 (GRCm39) A314S probably damaging Het
Gm6309 A G 5: 146,105,026 (GRCm39) S296P probably benign Het
Gmppb T G 9: 107,928,362 (GRCm39) V291G probably damaging Het
Hmcn1 G T 1: 150,619,492 (GRCm39) S1207R probably benign Het
Iars1 C T 13: 49,840,885 (GRCm39) P6L probably damaging Het
Kpna2 G A 11: 106,881,541 (GRCm39) T363I probably damaging Het
Lrp1b A T 2: 41,075,982 (GRCm39) H1886Q Het
Meak7 T C 8: 120,488,514 (GRCm39) E436G probably damaging Het
Mettl5 C T 2: 69,711,723 (GRCm39) D48N probably benign Het
Mfsd4a C T 1: 131,969,628 (GRCm39) G442S probably damaging Het
Mief2 A G 11: 60,622,074 (GRCm39) T215A probably damaging Het
Myt1 C T 2: 181,452,135 (GRCm39) T824I probably damaging Het
Naprt C A 15: 75,765,281 (GRCm39) V148L possibly damaging Het
Nckap1l C T 15: 103,382,277 (GRCm39) R491C probably damaging Het
Nr1i2 A G 16: 38,071,573 (GRCm39) M321T possibly damaging Het
Nup107 A T 10: 117,610,383 (GRCm39) I355N possibly damaging Het
Or10j2 G A 1: 173,098,183 (GRCm39) G147D possibly damaging Het
Or10x4 A T 1: 174,218,898 (GRCm39) N88Y probably benign Het
Or1e28-ps1 A G 11: 73,615,658 (GRCm39) I64T probably benign Het
Or1l4b T G 2: 37,036,518 (GRCm39) M98R probably damaging Het
Or4a80 T G 2: 89,582,636 (GRCm39) I179L probably benign Het
Or4k35 T G 2: 111,100,287 (GRCm39) I142L probably benign Het
Pccb T C 9: 100,876,634 (GRCm39) D320G possibly damaging Het
Pcdhgb6 A T 18: 37,875,561 (GRCm39) I90L probably benign Het
Pik3r2 A G 8: 71,221,459 (GRCm39) S682P probably damaging Het
Pkd1l3 GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA 8: 110,350,827 (GRCm39) probably benign Het
Plagl1 A G 10: 13,004,466 (GRCm39) Q578R unknown Het
Ppp1r42 A G 1: 10,073,563 (GRCm39) I9T probably benign Het
Ptcd3 A T 6: 71,871,275 (GRCm39) I315K possibly damaging Het
Rnf217 A G 10: 31,484,402 (GRCm39) L260P probably damaging Het
Selp A T 1: 163,968,975 (GRCm39) H525L possibly damaging Het
Sh3rf2 T A 18: 42,244,347 (GRCm39) M303K probably benign Het
Shprh A T 10: 11,082,076 (GRCm39) I1549F probably damaging Het
Slc38a7 G T 8: 96,570,772 (GRCm39) A244D probably benign Het
Stxbp6 G T 12: 44,949,740 (GRCm39) T63K probably damaging Het
Syne3 A G 12: 104,898,468 (GRCm39) S962P probably damaging Het
Syt10 T C 15: 89,711,135 (GRCm39) I133V probably damaging Het
Tars1 T A 15: 11,394,446 (GRCm39) K64* probably null Het
Tcaf3 A T 6: 42,566,636 (GRCm39) W818R probably damaging Het
Tekt2 C T 4: 126,217,444 (GRCm39) R207H probably damaging Het
Tmem70 A C 1: 16,735,659 (GRCm39) E43A probably benign Het
Trim72 C A 7: 127,609,092 (GRCm39) A298E probably damaging Het
Washc5 C T 15: 59,218,062 (GRCm39) probably null Het
Zfp707 C A 15: 75,847,085 (GRCm39) F378L possibly damaging Het
Zfp839 G A 12: 110,822,280 (GRCm39) A365T probably 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
R5374: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
Predicted Primers PCR Primer
(F):5'- TGGTTCTGAGTAGAAAGGGTGA -3'
(R):5'- TTAAGGGCAGAGGAAGCTGT -3'

Sequencing Primer
(F):5'- AGTAGAAAGGGTGAGGATTTTACTC -3'
(R):5'- GCTGTAGGAATAGAGTAAAATGGAG -3'
Posted On 2022-10-06