Incidental Mutation 'R1884:Gcm1'
ID 209359
Institutional Source Beutler Lab
Gene Symbol Gcm1
Ensembl Gene ENSMUSG00000023333
Gene Name glial cells missing homolog 1
Synonyms glial cell deficient, Gcm 1, Gcm a, GCMa, glide, Gcm1-rs1
MMRRC Submission 039905-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1884 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 77959240-77972906 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 77966861 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Leucine at position 27 (V27L)
Ref Sequence ENSEMBL: ENSMUSP00000024104 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000024104]
AlphaFold P70348
PDB Structure STRUCTURE OF THE GCM DOMAIN BOUND TO DNA [X-RAY DIFFRACTION]
Predicted Effect probably benign
Transcript: ENSMUST00000024104
AA Change: V27L

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000024104
Gene: ENSMUSG00000023333
AA Change: V27L

DomainStartEndE-ValueType
Pfam:GCM 30 167 4.2e-75 PFAM
Meta Mutation Damage Score 0.0733 question?
Coding Region Coverage
  • 1x: 97.3%
  • 3x: 96.7%
  • 10x: 95.1%
  • 20x: 92.3%
Validation Efficiency 99% (94/95)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a DNA-binding protein with a gcm-motif (glial cell missing motif). The encoded protein is a homolog of the Drosophila glial cells missing gene (gcm). This protein binds to the GCM-motif (A/G)CCCGCAT, a novel sequence among known targets of DNA-binding proteins. The N-terminal DNA-binding domain confers the unique DNA-binding activity of this protein. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations exhibit impaired branching of the chorioallantoic interface, absence of the placental labyrinth, lack of fusion of chorionic trophoblast cells, and lethality between embryonic days 5.5-10. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acad11 T C 9: 103,991,684 (GRCm39) M573T probably benign Het
Ank3 A G 10: 69,851,422 (GRCm39) T1162A possibly damaging Het
Anxa2 TCCC TCC 9: 69,397,036 (GRCm39) probably null Het
Arpp21 T A 9: 111,972,595 (GRCm39) D232V probably damaging Het
Atg2a T C 19: 6,304,414 (GRCm39) Y1144H probably damaging Het
Auh G A 13: 52,989,532 (GRCm39) P308L probably benign Het
Brs3 T C X: 56,092,449 (GRCm39) I311T probably benign Het
Cenpf C T 1: 189,379,046 (GRCm39) V2915I probably benign Het
Cep170 G T 1: 176,602,245 (GRCm39) T287K probably benign Het
Chst2 G A 9: 95,287,611 (GRCm39) T245I probably damaging Het
Cnot4 C T 6: 35,055,092 (GRCm39) V66I probably damaging Het
Cntn4 A G 6: 106,656,353 (GRCm39) T885A probably benign Het
Col20a1 C T 2: 180,634,703 (GRCm39) T131I possibly damaging Het
Coro7 G T 16: 4,446,683 (GRCm39) probably benign Het
Cpne8 C A 15: 90,532,831 (GRCm39) probably benign Het
Dbnl G A 11: 5,749,247 (GRCm39) G356E probably benign Het
Ddx31 T A 2: 28,749,002 (GRCm39) I266N probably damaging Het
Dnah7a A T 1: 53,580,159 (GRCm39) I1592N probably damaging Het
Dok6 A T 18: 89,492,130 (GRCm39) L149Q probably damaging Het
Eri2 G A 7: 119,390,346 (GRCm39) T94I probably benign Het
Ermp1 A G 19: 29,594,079 (GRCm39) V697A probably benign Het
Foxc1 C T 13: 31,991,648 (GRCm39) T153M probably damaging Het
Fry A G 5: 150,326,985 (GRCm39) I1224V probably benign Het
Fzd5 G A 1: 64,774,813 (GRCm39) T316M probably damaging Het
Gm5773 A T 3: 93,681,348 (GRCm39) D340V probably benign Het
Gucy2d T A 7: 98,100,815 (GRCm39) H379Q probably benign Het
Hectd1 T A 12: 51,847,738 (GRCm39) M392L probably benign Het
Itpr2 A C 6: 146,287,469 (GRCm39) D452E probably benign Het
Krtap2-4 G C 11: 99,505,505 (GRCm39) probably benign Het
Lrit1 T C 14: 36,783,710 (GRCm39) V346A possibly damaging Het
Lrrk1 A G 7: 65,912,185 (GRCm39) S1792P probably benign Het
Marveld2 A T 13: 100,737,129 (GRCm39) V168E probably benign Het
Ms4a4b T A 19: 11,438,629 (GRCm39) D149E probably damaging Het
Myom2 G A 8: 15,164,278 (GRCm39) D1058N probably benign Het
Ncam2 C T 16: 81,234,571 (GRCm39) P142L probably damaging Het
Nek9 A G 12: 85,379,330 (GRCm39) L192P probably damaging Het
Nol10 T C 12: 17,418,390 (GRCm39) probably null Het
Nrcam T C 12: 44,591,538 (GRCm39) V194A probably damaging Het
Nudt6 A G 3: 37,466,549 (GRCm39) V82A probably benign Het
Odf2l A T 3: 144,856,809 (GRCm39) N492I probably damaging Het
Or2a12 T C 6: 42,904,764 (GRCm39) S200P probably damaging Het
Or51f1d T C 7: 102,701,189 (GRCm39) I228T probably benign Het
Pkn3 T C 2: 29,972,840 (GRCm39) V276A probably damaging Het
Prl3b1 T G 13: 27,431,886 (GRCm39) L137R possibly damaging Het
Rab11fip2 A G 19: 59,925,762 (GRCm39) F10L probably damaging Het
Rab3b T A 4: 108,786,649 (GRCm39) V133E probably damaging Het
Rnf111 A T 9: 70,383,520 (GRCm39) S138T probably damaging Het
Rsf1 G A 7: 97,229,117 (GRCm39) probably benign Het
Runx1t1 A G 4: 13,835,767 (GRCm39) T75A probably benign Het
Ryr2 T G 13: 11,753,242 (GRCm39) K1693T probably damaging Het
Sdha A T 13: 74,481,255 (GRCm39) I317N probably damaging Het
Serpina1d T A 12: 103,732,037 (GRCm39) D274V possibly damaging Het
Setd2 T G 9: 110,385,486 (GRCm39) probably null Het
Sh3tc2 A G 18: 62,141,646 (GRCm39) Y1109C probably damaging Het
Sik3 C G 9: 46,132,387 (GRCm39) H1276Q probably benign Het
Slc22a2 A G 17: 12,833,713 (GRCm39) probably benign Het
Slc35f4 A T 14: 49,551,091 (GRCm39) W108R probably damaging Het
Slc4a1ap A G 5: 31,691,524 (GRCm39) E440G probably damaging Het
Slc6a4 A G 11: 76,904,201 (GRCm39) T219A probably benign Het
Stxbp5 C A 10: 9,688,042 (GRCm39) V420F possibly damaging Het
Svil T G 18: 5,094,640 (GRCm39) V1440G possibly damaging Het
Tas2r126 A T 6: 42,411,961 (GRCm39) T165S probably benign Het
Tbck T C 3: 132,430,677 (GRCm39) probably null Het
Tnxb T A 17: 34,908,539 (GRCm39) D1520E probably benign Het
Top1mt C T 15: 75,539,750 (GRCm39) R287H possibly damaging Het
Trdn A G 10: 33,133,091 (GRCm39) K314E probably benign Het
Troap T A 15: 98,975,779 (GRCm39) C233S probably benign Het
Usp28 T C 9: 48,947,247 (GRCm39) M571T probably damaging Het
Vac14 A G 8: 111,438,319 (GRCm39) H644R probably damaging Het
Vipr1 C T 9: 121,494,930 (GRCm39) P327L possibly damaging Het
Vmn1r31 C T 6: 58,449,029 (GRCm39) V279I probably damaging Het
Vmn1r69 G A 7: 10,314,678 (GRCm39) R18W probably benign Het
Vmn2r18 G T 5: 151,499,190 (GRCm39) Q425K probably benign Het
Vmn2r60 T C 7: 41,786,094 (GRCm39) V299A probably damaging Het
Vps13b A T 15: 35,430,437 (GRCm39) probably benign Het
Zfp157 A G 5: 138,443,102 (GRCm39) D31G probably damaging Het
Zfp385c A C 11: 100,521,532 (GRCm39) V176G probably benign Het
Zfp831 A G 2: 174,545,870 (GRCm39) H1325R possibly damaging Het
Other mutations in Gcm1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00690:Gcm1 APN 9 77,972,298 (GRCm39) missense probably benign 0.09
IGL02132:Gcm1 APN 9 77,972,121 (GRCm39) missense possibly damaging 0.95
IGL02820:Gcm1 APN 9 77,971,844 (GRCm39) missense probably benign
IGL03074:Gcm1 APN 9 77,972,057 (GRCm39) missense possibly damaging 0.84
PIT4280001:Gcm1 UTSW 9 77,966,915 (GRCm39) missense probably damaging 1.00
R0720:Gcm1 UTSW 9 77,971,923 (GRCm39) missense possibly damaging 0.68
R1271:Gcm1 UTSW 9 77,966,859 (GRCm39) missense probably benign 0.05
R1421:Gcm1 UTSW 9 77,966,982 (GRCm39) missense probably damaging 1.00
R1481:Gcm1 UTSW 9 77,966,999 (GRCm39) nonsense probably null
R1907:Gcm1 UTSW 9 77,972,055 (GRCm39) missense probably benign 0.00
R2029:Gcm1 UTSW 9 77,972,326 (GRCm39) missense possibly damaging 0.70
R2160:Gcm1 UTSW 9 77,968,662 (GRCm39) missense probably benign 0.05
R3103:Gcm1 UTSW 9 77,971,734 (GRCm39) missense probably damaging 0.98
R3944:Gcm1 UTSW 9 77,967,098 (GRCm39) nonsense probably null
R5292:Gcm1 UTSW 9 77,968,708 (GRCm39) missense probably damaging 1.00
R5769:Gcm1 UTSW 9 77,972,249 (GRCm39) missense probably benign
R6446:Gcm1 UTSW 9 77,967,065 (GRCm39) missense probably benign 0.08
R6465:Gcm1 UTSW 9 77,972,151 (GRCm39) missense probably damaging 0.99
R7114:Gcm1 UTSW 9 77,967,061 (GRCm39) missense probably damaging 1.00
R7212:Gcm1 UTSW 9 77,966,925 (GRCm39) missense possibly damaging 0.84
R7398:Gcm1 UTSW 9 77,971,961 (GRCm39) missense probably benign 0.00
R7584:Gcm1 UTSW 9 77,971,749 (GRCm39) missense possibly damaging 0.62
R8130:Gcm1 UTSW 9 77,971,816 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- ACACCTTGTCGCTAGTGTGC -3'
(R):5'- TCAGGTAAATCTTGCGGCCTTC -3'

Sequencing Primer
(F):5'- TTTCACAGGGGGCATCCAAGAC -3'
(R):5'- TCTGTGGAGCAGTCCCTG -3'
Posted On 2014-06-30