Incidental Mutation 'R3900:Khdc3'
ID 474452
Institutional Source Beutler Lab
Gene Symbol Khdc3
Ensembl Gene ENSMUSG00000092622
Gene Name KH domain containing 3, subcortical maternal complex member
Synonyms FILIA, ecat1, 2410004A20Rik
MMRRC Submission 041607-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.094) question?
Stock # R3900 (G1)
Quality Score 225
Status Not validated
Chromosome 9
Chromosomal Location 73009118-73011720 bp(+) (GRCm39)
Type of Mutation intron
DNA Base Change (assembly) T to C at 73011628 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000134473 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034737] [ENSMUST00000167514] [ENSMUST00000172578] [ENSMUST00000173734] [ENSMUST00000174203]
AlphaFold Q9CWU5
Predicted Effect probably benign
Transcript: ENSMUST00000034737
SMART Domains Protein: ENSMUSP00000034737
Gene: ENSMUSG00000092622

DomainStartEndE-ValueType
Pfam:MOEP19 28 113 4.5e-34 PFAM
internal_repeat_1 117 217 6.81e-11 PROSPERO
internal_repeat_1 218 316 6.81e-11 PROSPERO
internal_repeat_2 275 397 3.62e-8 PROSPERO
Predicted Effect probably benign
Transcript: ENSMUST00000167514
SMART Domains Protein: ENSMUSP00000132527
Gene: ENSMUSG00000092622

DomainStartEndE-ValueType
internal_repeat_1 117 212 2.21e-8 PROSPERO
internal_repeat_1 207 356 2.21e-8 PROSPERO
Predicted Effect probably benign
Transcript: ENSMUST00000172578
SMART Domains Protein: ENSMUSP00000133850
Gene: ENSMUSG00000092622

DomainStartEndE-ValueType
PDB:3V69|B 1 75 4e-49 PDB
Predicted Effect unknown
Transcript: ENSMUST00000173734
AA Change: S342P
SMART Domains Protein: ENSMUSP00000133915
Gene: ENSMUSG00000092622
AA Change: S342P

DomainStartEndE-ValueType
internal_repeat_2 116 194 1.27e-8 PROSPERO
internal_repeat_1 117 231 1.6e-13 PROSPERO
internal_repeat_1 231 341 1.6e-13 PROSPERO
internal_repeat_2 267 344 1.27e-8 PROSPERO
Predicted Effect probably benign
Transcript: ENSMUST00000174203
SMART Domains Protein: ENSMUSP00000134473
Gene: ENSMUSG00000092310

DomainStartEndE-ValueType
internal_repeat_1 116 173 5.47e-9 PROSPERO
internal_repeat_1 177 233 5.47e-9 PROSPERO
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.4%
Validation Efficiency 98% (45/46)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene belongs to the KHDC1 family, members of which contain an atypical KH domain that may not bind RNA like canonical KH domains. This gene is specifically expressed in the oocytes, and recent studies suggest that it may function as a regulator of genomic imprinting in the oocyte. Mutations in this gene are associated with recurrent biparental complete hydatidiform mole. [provided by RefSeq, Dec 2011]
PHENOTYPE: Homozygous null mice display a maternal effect defect in embryogenesis with delayed embryonic development and spindle abnormalities resulting in decreased litter sizes for homozygous females. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4833439L19Rik A T 13: 54,700,781 (GRCm39) S212R probably damaging Het
AI182371 T C 2: 34,975,228 (GRCm39) I334V probably benign Het
Anpep A G 7: 79,488,973 (GRCm39) S372P probably benign Het
Apc2 C A 10: 80,131,806 (GRCm39) probably null Het
Bcl6 T G 16: 23,796,304 (GRCm39) E41A possibly damaging Het
Brpf1 A G 6: 113,295,394 (GRCm39) I674V probably benign Het
Cherp A G 8: 73,223,780 (GRCm39) I201T possibly damaging Het
Cluh A G 11: 74,557,930 (GRCm39) H1056R probably benign Het
Csgalnact2 A T 6: 118,097,975 (GRCm39) F122I probably damaging Het
Cubn C A 2: 13,291,791 (GRCm39) probably null Het
Dnah17 A T 11: 117,985,634 (GRCm39) I1481N possibly damaging Het
Eif2ak4 A G 2: 118,305,510 (GRCm39) Y1561C probably damaging Het
Elfn1 G A 5: 139,957,719 (GRCm39) R241H probably damaging Het
Eml5 G A 12: 98,791,782 (GRCm39) R1245C probably damaging Het
Fchsd2 A G 7: 100,841,006 (GRCm39) K172E possibly damaging Het
Gm10608 CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 9: 118,989,784 (GRCm39) probably null Het
Gm6133 A G 18: 78,393,365 (GRCm39) N120D probably benign Het
Hivep2 C A 10: 14,004,713 (GRCm39) T437K probably benign Het
Igsf9 T C 1: 172,317,125 (GRCm39) L35P probably damaging Het
Mmrn2 G T 14: 34,121,517 (GRCm39) probably null Het
Mrgpra1 G T 7: 46,985,275 (GRCm39) R135S possibly damaging Het
Or4c11b A T 2: 88,625,273 (GRCm39) L182F possibly damaging Het
Or8g2b A G 9: 39,750,698 (GRCm39) probably null Het
Otud3 T C 4: 138,624,196 (GRCm39) N282S probably benign Het
Prkar1a A G 11: 109,551,901 (GRCm39) K130R probably benign Het
Rd3 T C 1: 191,717,217 (GRCm39) V114A probably damaging Het
Rictor T G 15: 6,818,954 (GRCm39) D1392E probably benign Het
Setd2 C T 9: 110,421,586 (GRCm39) R273W probably damaging Het
Slc22a18 C A 7: 143,033,507 (GRCm39) A86E probably damaging Het
Slc24a1 A T 9: 64,835,426 (GRCm39) S900R probably damaging Het
Smarcc1 T C 9: 109,947,586 (GRCm39) probably benign Het
Smoc1 T C 12: 81,214,287 (GRCm39) V234A probably damaging Het
Stard9 A G 2: 120,544,030 (GRCm39) T4443A possibly damaging Het
Timp2 C T 11: 118,194,542 (GRCm39) D139N probably damaging Het
Trim69 A G 2: 122,009,322 (GRCm39) T461A probably benign Het
Ubash3b C T 9: 40,942,860 (GRCm39) D211N probably benign Het
Ubr4 T C 4: 139,206,373 (GRCm39) probably null Het
Ubr5 T C 15: 38,019,486 (GRCm39) D752G probably damaging Het
Urb1 A T 16: 90,580,264 (GRCm39) I633N possibly damaging Het
Usp36 T A 11: 118,170,650 (GRCm39) D28V possibly damaging Het
Wdr6 G A 9: 108,452,968 (GRCm39) A305V probably damaging Het
Zfp248 T C 6: 118,406,527 (GRCm39) N253S probably damaging Het
Other mutations in Khdc3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02987:Khdc3 APN 9 73,009,948 (GRCm39) missense possibly damaging 0.56
R1487:Khdc3 UTSW 9 73,009,846 (GRCm39) missense probably benign 0.19
R1523:Khdc3 UTSW 9 73,010,773 (GRCm39) missense possibly damaging 0.53
R1545:Khdc3 UTSW 9 73,010,942 (GRCm39) missense probably benign 0.05
R1951:Khdc3 UTSW 9 73,010,519 (GRCm39) missense possibly damaging 0.48
R2935:Khdc3 UTSW 9 73,010,987 (GRCm39) missense possibly damaging 0.92
R3076:Khdc3 UTSW 9 73,010,212 (GRCm39) missense probably damaging 1.00
R3880:Khdc3 UTSW 9 73,010,872 (GRCm39) missense possibly damaging 0.73
R3899:Khdc3 UTSW 9 73,011,628 (GRCm39) intron probably benign
R4224:Khdc3 UTSW 9 73,010,153 (GRCm39) missense possibly damaging 0.92
R4412:Khdc3 UTSW 9 73,010,156 (GRCm39) missense possibly damaging 0.93
R4529:Khdc3 UTSW 9 73,011,301 (GRCm39) missense possibly damaging 0.83
R4647:Khdc3 UTSW 9 73,009,868 (GRCm39) missense possibly damaging 0.81
R4648:Khdc3 UTSW 9 73,009,868 (GRCm39) missense possibly damaging 0.81
R5153:Khdc3 UTSW 9 73,010,720 (GRCm39) missense probably benign 0.18
R5261:Khdc3 UTSW 9 73,010,768 (GRCm39) missense possibly damaging 0.92
R8362:Khdc3 UTSW 9 73,010,848 (GRCm39) missense possibly damaging 0.96
X0024:Khdc3 UTSW 9 73,011,206 (GRCm39) missense probably benign 0.01
X0026:Khdc3 UTSW 9 73,010,265 (GRCm39) missense possibly damaging 0.95
X0066:Khdc3 UTSW 9 73,011,463 (GRCm39) missense probably benign 0.00
Predicted Primers
Posted On 2017-04-14