Incidental Mutation 'R5249:Kdm5d'
ID 398895
Institutional Source Beutler Lab
Gene Symbol Kdm5d
Ensembl Gene ENSMUSG00000056673
Gene Name lysine demethylase 5D
Synonyms Smcy, HY, Jarid1d
MMRRC Submission 042820-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.071) question?
Stock # R5249 (G1)
Quality Score 222
Status Validated
Chromosome Y
Chromosomal Location 897566-943813 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 916692 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 391 (Y391H)
Ref Sequence ENSEMBL: ENSMUSP00000139636 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000055032] [ENSMUST00000186696] [ENSMUST00000186726] [ENSMUST00000189069]
AlphaFold Q62240
Predicted Effect possibly damaging
Transcript: ENSMUST00000055032
AA Change: Y391H

PolyPhen 2 Score 0.700 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: Y391H

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 possibly damaging
Transcript: ENSMUST00000186696
AA Change: Y391H

PolyPhen 2 Score 0.700 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000140663
Gene: ENSMUSG00000056673
AA Change: Y391H

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000188910
Predicted Effect probably damaging
Transcript: ENSMUST00000189069
AA Change: Y391H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000139636
Gene: ENSMUSG00000056673
AA Change: Y391H

DomainStartEndE-ValueType
JmjN 13 54 3.45e-23 SMART
ARID 76 165 4.84e-36 SMART
BRIGHT 80 170 4.48e-38 SMART
Blast:ARID 175 298 1e-46 BLAST
PHD 325 371 8.56e-13 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000189626
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.8%
Validation Efficiency 98% (93/95)
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: 89 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A4gnt A G 9: 99,502,284 (GRCm39) H148R probably damaging Het
Acrbp A G 6: 125,037,885 (GRCm39) D394G probably damaging Het
Adam18 T C 8: 25,115,868 (GRCm39) T609A probably benign Het
Adam25 T A 8: 41,208,991 (GRCm39) N752K probably benign Het
Ano6 A C 15: 95,811,469 (GRCm39) S176R probably benign Het
Ano7 T C 1: 93,302,918 (GRCm39) S19P probably benign Het
Ap1b1 A G 11: 4,976,364 (GRCm39) E437G probably damaging Het
Arfgap2 T A 2: 91,095,982 (GRCm39) C46* probably null Het
Arhgef26 T A 3: 62,247,981 (GRCm39) L355Q probably damaging Het
B4galnt4 C T 7: 140,644,983 (GRCm39) T219I probably damaging Het
Bap1 C T 14: 30,979,243 (GRCm39) probably benign Het
Catip T G 1: 74,401,954 (GRCm39) L43R probably damaging Het
Ccdc177 G A 12: 80,805,282 (GRCm39) R331C unknown Het
Cep85l T C 10: 53,195,690 (GRCm39) probably null Het
Cfap206 T A 4: 34,714,502 (GRCm39) Q398L probably benign Het
Clec18a A G 8: 111,800,368 (GRCm39) C352R probably damaging Het
Clic6 A T 16: 92,336,339 (GRCm39) Y549F probably damaging Het
Cpne9 C T 6: 113,270,034 (GRCm39) probably benign Het
Cyb5r3 A C 15: 83,042,836 (GRCm39) probably benign Het
Dnah6 C T 6: 73,090,471 (GRCm39) R2293K probably damaging Het
Dnmbp C A 19: 43,890,879 (GRCm39) R296L probably damaging Het
Dtwd1 C A 2: 125,996,694 (GRCm39) Q60K probably benign Het
Esyt1 C A 10: 128,352,443 (GRCm39) V723L probably benign Het
Fbxo42 T C 4: 140,926,335 (GRCm39) L339P probably damaging Het
Furin A T 7: 80,043,169 (GRCm39) N347K probably damaging Het
Fzd7 T C 1: 59,522,522 (GRCm39) M135T probably damaging Het
Garin1b A G 6: 29,323,896 (GRCm39) D207G probably damaging Het
Hlf A G 11: 90,278,632 (GRCm39) M144T probably benign Het
Hyal5 C T 6: 24,876,648 (GRCm39) Q174* probably null Het
Kcnb1 T A 2: 166,947,103 (GRCm39) M582L possibly damaging Het
Khdc4 T A 3: 88,604,032 (GRCm39) I283N probably damaging Het
Kif21b C T 1: 136,096,966 (GRCm39) T1297M probably damaging Het
Krt8 T G 15: 101,906,875 (GRCm39) N317T possibly damaging Het
Lctl G T 9: 64,045,196 (GRCm39) V372L probably benign Het
Lig1 C T 7: 13,042,432 (GRCm39) H822Y possibly damaging Het
Lrrc4b A G 7: 44,111,988 (GRCm39) D620G possibly damaging Het
Mboat4 C T 8: 34,582,275 (GRCm39) H10Y probably benign Het
Med1 A T 11: 98,048,066 (GRCm39) M910K probably benign Het
Mia2 A T 12: 59,154,911 (GRCm39) D209V probably damaging Het
Mpp4 C T 1: 59,184,017 (GRCm39) probably benign Het
Mrgprb1 A T 7: 48,097,225 (GRCm39) V229E possibly damaging Het
Mtor T A 4: 148,548,189 (GRCm39) C485S probably damaging Het
Mx1 T C 16: 97,258,628 (GRCm39) D23G probably damaging Het
Myrfl T C 10: 116,619,138 (GRCm39) D740G probably benign Het
Myt1l G A 12: 29,882,331 (GRCm39) G509R unknown Het
Nav2 G A 7: 49,185,661 (GRCm39) V874I probably damaging Het
Ntrk3 A T 7: 78,110,914 (GRCm39) N262K possibly damaging Het
Opa1 A T 16: 29,437,077 (GRCm39) D699V probably damaging Het
Or10u4 C T 10: 129,802,078 (GRCm39) A164T probably benign Het
Or8b51 A G 9: 38,569,374 (GRCm39) C105R possibly damaging Het
Otud7a A G 7: 63,407,181 (GRCm39) N495D possibly damaging Het
Pcsk9 T C 4: 106,320,950 (GRCm39) D53G probably benign Het
Pdcd5 A G 7: 35,346,421 (GRCm39) probably benign Het
Phf21a C T 2: 92,058,822 (GRCm39) P28L probably damaging Het
Pitpnm1 T A 19: 4,158,130 (GRCm39) D573E probably damaging Het
Ppp1r35 C T 5: 137,777,406 (GRCm39) probably benign Het
Ptprq T C 10: 107,535,496 (GRCm39) Q423R probably damaging Het
Pum1 A T 4: 130,490,125 (GRCm39) Y699F probably benign Het
Rabgef1 A G 5: 130,241,841 (GRCm39) D415G probably benign Het
Rapgef6 A G 11: 54,413,943 (GRCm39) E23G probably benign Het
Rpia G T 6: 70,760,563 (GRCm39) C121* probably null Het
Sanbr A G 11: 23,525,483 (GRCm39) *719Q probably null Het
Serpinb13 T A 1: 106,926,427 (GRCm39) W201R probably damaging Het
Sh3bp4 T C 1: 89,065,456 (GRCm39) C17R probably damaging Het
Sh3d21 A G 4: 126,055,858 (GRCm39) probably benign Het
Slamf6 A C 1: 171,764,249 (GRCm39) N214T probably damaging Het
Slc7a2 T C 8: 41,361,130 (GRCm39) Y365H possibly damaging Het
Sox18 T C 2: 181,312,971 (GRCm39) probably null Het
Spink7 A T 18: 62,725,507 (GRCm39) F79I possibly damaging Het
Srpk3 C T X: 72,818,555 (GRCm39) R82* probably null Het
Sspo A T 6: 48,470,244 (GRCm39) H4561L probably damaging Het
Tcaf1 T C 6: 42,653,793 (GRCm39) K700R probably benign Het
Tcf25 G T 8: 124,115,372 (GRCm39) R203L probably damaging Het
Tcp11 T C 17: 28,290,757 (GRCm39) I201V possibly damaging Het
Tex2 T C 11: 106,437,615 (GRCm39) D685G unknown Het
Themis G T 10: 28,637,195 (GRCm39) E100* probably null Het
Tmem52b G A 6: 129,491,221 (GRCm39) probably null Het
Tnr C T 1: 159,512,226 (GRCm39) probably benign Het
Tox3 T C 8: 90,975,444 (GRCm39) I396V probably benign Het
Tpm2 T A 4: 43,514,828 (GRCm39) E269V probably benign Het
Tulp1 C T 17: 28,581,651 (GRCm39) probably benign Het
Tymp GC GCC 15: 89,258,567 (GRCm39) probably null Het
Ube2j2 A C 4: 156,033,515 (GRCm39) K30Q possibly damaging Het
Usp19 T A 9: 108,369,807 (GRCm39) M1K probably null Het
Vmn2r52 C A 7: 9,910,197 (GRCm39) R6L probably benign Het
Zbed4 G A 15: 88,665,290 (GRCm39) V453M probably benign Het
Zfp319 T C 8: 96,055,099 (GRCm39) E368G probably benign Het
Zfp366 A C 13: 99,366,117 (GRCm39) E426A probably damaging Het
Zfp687 A T 3: 94,916,777 (GRCm39) I783N 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
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
R9668:Kdm5d UTSW Y 943,075 (GRCm39) missense possibly damaging 0.73
Predicted Primers PCR Primer
(F):5'- CAGTGTGTTCAAGGCAGCTC -3'
(R):5'- GAATTCCTTTTCCACAACTTCTGTAGG -3'

Sequencing Primer
(F):5'- GTTCAAGGCAGCTCTTAGTTTC -3'
(R):5'- CACAACTTCTGTAGGTACCATCTATG -3'
Posted On 2016-07-06