Incidental Mutation 'R5769:Gcm1'
ID 446444
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 043369-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5769 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 77959240-77972906 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 77972249 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 397 (T397A)
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: T397A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000024104
Gene: ENSMUSG00000023333
AA Change: T397A

DomainStartEndE-ValueType
Pfam:GCM 30 167 4.2e-75 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000217247
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.8%
Validation Efficiency 98% (65/66)
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: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A430033K04Rik T A 5: 138,644,595 (GRCm39) V160E possibly damaging Het
Abcb1a A C 5: 8,733,426 (GRCm39) E106A probably benign Het
Acap3 A T 4: 155,986,857 (GRCm39) D371V probably damaging Het
Ahi1 T C 10: 20,835,981 (GRCm39) probably null Het
Coq8a A G 1: 180,006,681 (GRCm39) Y69H probably damaging Het
Defb33 T A 8: 21,387,543 (GRCm39) F27I possibly damaging Het
Dhx29 T A 13: 113,090,251 (GRCm39) L776Q probably damaging Het
Dnah3 G A 7: 119,689,175 (GRCm39) R80* probably null Het
Dtna A T 18: 23,784,611 (GRCm39) D646V probably benign Het
Eml5 T A 12: 98,756,878 (GRCm39) D1964V probably damaging Het
Fbn2 A T 18: 58,238,271 (GRCm39) N575K probably damaging Het
Fbxo38 G A 18: 62,648,036 (GRCm39) P834L probably benign Het
Fyb2 G T 4: 104,870,518 (GRCm39) K706N probably damaging Het
Fyb2 T A 4: 104,872,841 (GRCm39) V738E probably damaging Het
Gins1 A T 2: 150,767,918 (GRCm39) E149D probably damaging Het
Gm11595 G A 11: 99,663,381 (GRCm39) R100C unknown Het
Grin2a C T 16: 9,579,390 (GRCm39) R291K possibly damaging Het
Hdac10 T C 15: 89,007,819 (GRCm39) M646V probably benign Het
Hes6 G T 1: 91,340,671 (GRCm39) R38S probably damaging Het
Hipk3 G A 2: 104,265,298 (GRCm39) P667S possibly damaging Het
Jrk T C 15: 74,577,917 (GRCm39) Q456R probably benign Het
Klf18 A C 4: 117,586,162 (GRCm39) probably benign Het
Loxl3 A G 6: 83,027,581 (GRCm39) T708A probably damaging Het
Lyg1 T C 1: 37,989,831 (GRCm39) S19G unknown Het
Magel2 T A 7: 62,027,861 (GRCm39) M255K probably benign Het
Mctp1 A G 13: 76,907,927 (GRCm39) D242G probably damaging Het
Med13 A T 11: 86,236,829 (GRCm39) N109K probably benign Het
Mms19 A G 19: 41,952,825 (GRCm39) F95L probably damaging Het
Nav1 A G 1: 135,379,995 (GRCm39) L1569P probably damaging Het
Nup188 A G 2: 30,220,747 (GRCm39) E940G probably benign Het
Oas1d T C 5: 121,054,917 (GRCm39) F163S probably benign Het
Odf2l A G 3: 144,841,492 (GRCm39) K304R possibly damaging Het
Otud3 T A 4: 138,625,421 (GRCm39) N211I possibly damaging Het
Pabpc6 A T 17: 9,886,772 (GRCm39) L593* probably null Het
Pdcd11 T A 19: 47,091,076 (GRCm39) L350Q possibly damaging Het
Pdia4 A G 6: 47,792,446 (GRCm39) probably benign Het
Pik3cb G A 9: 98,975,212 (GRCm39) Q223* probably null Het
Plb1 G A 5: 32,474,866 (GRCm39) V696M probably benign Het
Ppp2r5a T C 1: 191,104,863 (GRCm39) D61G probably benign Het
Preb G T 5: 31,115,635 (GRCm39) Y87* probably null Het
Rdh16f2 A T 10: 127,712,758 (GRCm39) N252I probably benign Het
Rida T C 15: 34,484,704 (GRCm39) probably benign Het
Rxrb T C 17: 34,251,821 (GRCm39) probably benign Het
Sis T A 3: 72,835,568 (GRCm39) K931N probably damaging Het
Srcap T A 7: 127,158,994 (GRCm39) probably benign Het
Srp68 A G 11: 116,137,495 (GRCm39) S525P probably damaging Het
Susd2 C T 10: 75,473,853 (GRCm39) A581T probably damaging Het
Synj1 A G 16: 90,735,141 (GRCm39) probably benign Het
Syt12 T C 19: 4,501,072 (GRCm39) Y326C probably damaging Het
Tesk2 A G 4: 116,659,512 (GRCm39) probably null Het
Tmem41b G A 7: 109,577,945 (GRCm39) T113I possibly damaging Het
Tmtc2 T C 10: 105,205,907 (GRCm39) I463V probably benign Het
Trak1 A T 9: 121,277,904 (GRCm39) D320V probably damaging Het
Ushbp1 A T 8: 71,838,863 (GRCm39) N570K probably benign Het
Vmn1r33 T A 6: 66,588,817 (GRCm39) I246F possibly damaging Het
Vmn2r54 A C 7: 12,349,209 (GRCm39) L791R possibly damaging Het
Washc1 A T 17: 66,425,111 (GRCm39) T372S probably benign Het
Zfp1005 A G 2: 150,110,198 (GRCm39) E296G 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
R1884:Gcm1 UTSW 9 77,966,861 (GRCm39) missense probably benign 0.01
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
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'- TTACCCCAGCAAGTTCCATCAG -3'
(R):5'- ACATTCCTCTCAGGCTATGC -3'

Sequencing Primer
(F):5'- TTCCATCAGAACCCCCTGCAG -3'
(R):5'- AGGCTATGCTTTGAAACCCG -3'
Posted On 2016-11-21