Incidental Mutation 'R4679:C9orf72'
ID 349903
Institutional Source Beutler Lab
Gene Symbol C9orf72
Ensembl Gene ENSMUSG00000028300
Gene Name C9orf72, member of C9orf72-SMCR8 complex
Synonyms Dennd9, 3110043O21Rik
MMRRC Submission 041932-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4679 (G1)
Quality Score 225
Status Validated
Chromosome 4
Chromosomal Location 35191285-35226153 bp(-) (GRCm39)
Type of Mutation unclassified
DNA Base Change (assembly) C to T at 35226033 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000103762 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000084724] [ENSMUST00000108126] [ENSMUST00000108127]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000084724
SMART Domains Protein: ENSMUSP00000081775
Gene: ENSMUSG00000028300

DomainStartEndE-ValueType
Pfam:C9orf72-like 60 325 6.8e-90 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000108126
SMART Domains Protein: ENSMUSP00000103761
Gene: ENSMUSG00000028300

DomainStartEndE-ValueType
Pfam:C9orf72-like 1 161 2e-56 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000108127
SMART Domains Protein: ENSMUSP00000103762
Gene: ENSMUSG00000028300

DomainStartEndE-ValueType
Pfam:C9orf72-like 61 324 1.9e-99 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000127015
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130538
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146909
Predicted Effect noncoding transcript
Transcript: ENSMUST00000149677
Predicted Effect noncoding transcript
Transcript: ENSMUST00000149138
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156472
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.7%
  • 20x: 93.9%
Validation Efficiency 98% (112/114)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene plays an important role in the regulation of endosomal trafficking, and has been shown to interact with Rab proteins that are involved in autophagy and endocytic transport. Expansion of a GGGGCC repeat from 2-22 copies to 700-1600 copies in the intronic sequence between alternate 5' exons in transcripts from this gene is associated with 9p-linked ALS (amyotrophic lateral sclerosis) and FTD (frontotemporal dementia) (PMID: 21944778, 21944779). Studies suggest that hexanucleotide expansions could result in the selective stabilization of repeat-containing pre-mRNA, and the accumulation of insoluble dipeptide repeat protein aggregates that could be pathogenic in FTD-ALS patients (PMID: 23393093). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2016]
PHENOTYPE: Nullizygous mice show splenomegaly and lymphadenopathy. Homozygotes for one allele show reduced body weight, hematocrit and hemoglobin content, lymphopenia, neutrophilia, social interaction deficits and premature death. Homozygotes for another allele show altered macrophage and microglia physiology. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 93 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
AA986860 T A 1: 130,670,140 (GRCm39) S121T possibly damaging Het
Abcb9 A G 5: 124,216,867 (GRCm39) V450A probably benign Het
Abcg1 A T 17: 31,333,235 (GRCm39) R659S probably benign Het
Acad9 A T 3: 36,142,989 (GRCm39) N508I possibly damaging Het
Acrbp T A 6: 125,037,881 (GRCm39) C393S probably damaging Het
Adcy7 T C 8: 89,044,565 (GRCm39) V486A probably benign Het
Adgrf1 G T 17: 43,621,384 (GRCm39) L540F probably damaging Het
Ap5m1 T C 14: 49,316,285 (GRCm39) I285T probably benign Het
Arhgap27 G T 11: 103,251,775 (GRCm39) probably benign Het
Armc5 A T 7: 127,839,276 (GRCm39) E198V possibly damaging Het
Atp8b5 A T 4: 43,365,955 (GRCm39) K742M probably benign Het
Atp9a T G 2: 168,503,884 (GRCm39) T603P possibly damaging Het
Bsn A G 9: 107,987,329 (GRCm39) S2808P unknown Het
Catsper4 T C 4: 133,953,916 (GRCm39) N81S probably damaging Het
Ccl17 C G 8: 95,537,128 (GRCm39) T10S probably benign Het
Cdc123 A T 2: 5,849,703 (GRCm39) V6D probably damaging Het
Cdca2 T C 14: 67,952,415 (GRCm39) K14E possibly damaging Het
Cdh3 C A 8: 107,266,488 (GRCm39) T302K probably damaging Het
Cdh9 A G 15: 16,851,045 (GRCm39) M605V probably benign Het
Cdk4 A G 10: 126,900,780 (GRCm39) E144G possibly damaging Het
Clasp1 C T 1: 118,471,001 (GRCm39) A879V probably damaging Het
Cldn8 G A 16: 88,359,296 (GRCm39) H210Y probably benign Het
Cntn5 T C 9: 9,970,536 (GRCm39) D518G probably benign Het
Cog1 C T 11: 113,543,116 (GRCm39) A208V probably damaging Het
Col4a2 T A 8: 11,481,337 (GRCm39) H836Q possibly damaging Het
Copb1 T C 7: 113,848,211 (GRCm39) D108G probably damaging Het
Csmd3 A T 15: 48,024,479 (GRCm39) Y600* probably null Het
Cyb5r1 T A 1: 134,335,571 (GRCm39) H164Q probably benign Het
Dkc1 A G X: 74,144,598 (GRCm39) I215V probably benign Het
Enpep A G 3: 129,097,362 (GRCm39) probably null Het
Fam110d A G 4: 133,978,747 (GRCm39) S244P probably damaging Het
Fbln7 A G 2: 128,736,806 (GRCm39) Y311C probably damaging Het
Fign A C 2: 63,809,605 (GRCm39) L555R probably damaging Het
Fkbp7 A T 2: 76,502,032 (GRCm39) probably benign Het
Fmn2 T C 1: 174,330,728 (GRCm39) S373P unknown Het
Frmd4b C T 6: 97,272,627 (GRCm39) D868N possibly damaging Het
Garin3 T A 11: 46,295,640 (GRCm39) M4K possibly damaging Het
Gfpt2 A G 11: 49,714,564 (GRCm39) N321S probably benign Het
Glmn G T 5: 107,708,941 (GRCm39) T372K probably damaging Het
Gm26602 C T 10: 79,746,808 (GRCm39) probably benign Het
Gm6797 A G X: 8,505,933 (GRCm39) noncoding transcript Het
Gpat3 T A 5: 101,041,322 (GRCm39) F383L probably damaging Het
H2-M11 C T 17: 36,859,042 (GRCm39) T194I possibly damaging Het
Hcn1 C T 13: 117,793,551 (GRCm39) H268Y probably benign Het
Hectd4 G T 5: 121,463,314 (GRCm39) C2345F possibly damaging Het
Htt A G 5: 34,977,424 (GRCm39) D770G probably benign Het
Ints3 T C 3: 90,315,817 (GRCm39) T316A possibly damaging Het
Ipo9 A G 1: 135,321,907 (GRCm39) F608L probably benign Het
Irak1 A C X: 73,065,995 (GRCm39) probably benign Het
Jam2 G A 16: 84,609,840 (GRCm39) V151M probably damaging Het
Lag3 T A 6: 124,881,508 (GRCm39) Q488L possibly damaging Het
Large2 A T 2: 92,197,903 (GRCm39) L266Q probably benign Het
Lrp3 T G 7: 34,903,365 (GRCm39) D327A probably damaging Het
Mamstr C A 7: 45,294,116 (GRCm39) probably benign Het
Mettl14 G A 3: 123,163,063 (GRCm39) probably benign Het
Miga1 A G 3: 152,028,112 (GRCm39) V139A probably damaging Het
Mthfd2l A C 5: 91,096,770 (GRCm39) R130S probably benign Het
Myo1b A G 1: 51,797,132 (GRCm39) I970T possibly damaging Het
Nat10 C A 2: 103,562,515 (GRCm39) W607L probably damaging Het
Nop56 A G 2: 130,120,193 (GRCm39) T183A probably benign Het
Or10h1 A G 17: 33,418,367 (GRCm39) H115R probably benign Het
Or2d4 A T 7: 106,544,152 (GRCm39) S19T probably benign Het
Or4c10 A G 2: 89,761,008 (GRCm39) Y285C possibly damaging Het
Or4d1 T A 11: 87,805,136 (GRCm39) M199L probably benign Het
Or52j3 A G 7: 102,836,309 (GRCm39) Y167C probably benign Het
Or5ae2 T A 7: 84,506,112 (GRCm39) Y178* probably null Het
Pcdhb12 T C 18: 37,570,002 (GRCm39) F383L probably damaging Het
Pde4dip C A 3: 97,602,321 (GRCm39) D2252Y probably damaging Het
Peg10 GC GCTCC 6: 4,756,452 (GRCm39) probably benign Het
Plscr2 T G 9: 92,169,823 (GRCm39) L91R probably benign Het
Plxnc1 T A 10: 94,630,306 (GRCm39) Y1531F probably damaging Het
Ptprq A T 10: 107,521,043 (GRCm39) F710I probably benign Het
Rad51ap2 A G 12: 11,506,552 (GRCm39) E158G probably damaging Het
Rasip1 T A 7: 45,277,247 (GRCm39) H18Q possibly damaging Het
Rcsd1 T A 1: 165,483,493 (GRCm39) N166I probably damaging Het
Ripor1 T A 8: 106,344,417 (GRCm39) I517K possibly damaging Het
Ryr2 T A 13: 11,839,255 (GRCm39) H506L probably benign Het
Secisbp2l C T 2: 125,582,657 (GRCm39) G933D possibly damaging Het
Septin14 T C 5: 129,770,090 (GRCm39) D202G possibly damaging Het
Siglec1 A T 2: 130,915,331 (GRCm39) L1420Q possibly damaging Het
Slc22a29 T A 19: 8,138,948 (GRCm39) I505F possibly damaging Het
Sorcs1 T A 19: 50,171,107 (GRCm39) Y927F probably benign Het
Spats2 T G 15: 99,078,603 (GRCm39) M191R possibly damaging Het
Sycp1 C T 3: 102,829,778 (GRCm39) probably null Het
T2 A G 17: 8,609,848 (GRCm39) E99G possibly damaging Het
Taf3 G A 2: 10,053,375 (GRCm39) probably benign Het
Tnfsf10 A T 3: 27,389,728 (GRCm39) N263I probably damaging Het
Treml2 A T 17: 48,615,203 (GRCm39) R229S probably benign Het
Trmt13 T C 3: 116,383,404 (GRCm39) K125E probably damaging Het
Ttc9 G T 12: 81,678,375 (GRCm39) C66F probably damaging Het
Vmn2r63 C T 7: 42,577,544 (GRCm39) M331I probably benign Het
Zfp353-ps T C 8: 42,535,251 (GRCm39) noncoding transcript Het
Zfp932 A T 5: 110,157,760 (GRCm39) H486L probably damaging Het
Other mutations in C9orf72
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00473:C9orf72 APN 4 35,213,616 (GRCm39) missense possibly damaging 0.57
IGL00718:C9orf72 APN 4 35,213,015 (GRCm39) missense probably damaging 1.00
IGL01284:C9orf72 APN 4 35,218,808 (GRCm39) missense probably damaging 0.96
IGL01998:C9orf72 APN 4 35,194,179 (GRCm39) missense probably benign 0.30
IGL02185:C9orf72 APN 4 35,197,046 (GRCm39) missense probably damaging 1.00
IGL02403:C9orf72 APN 4 35,205,887 (GRCm39) splice site probably benign
IGL02823:C9orf72 APN 4 35,213,031 (GRCm39) missense probably damaging 0.98
R0194:C9orf72 UTSW 4 35,197,207 (GRCm39) missense probably damaging 1.00
R0471:C9orf72 UTSW 4 35,193,257 (GRCm39) missense probably benign 0.01
R1172:C9orf72 UTSW 4 35,218,630 (GRCm39) missense probably damaging 0.99
R1175:C9orf72 UTSW 4 35,218,630 (GRCm39) missense probably damaging 0.99
R1765:C9orf72 UTSW 4 35,197,098 (GRCm39) missense probably damaging 1.00
R4326:C9orf72 UTSW 4 35,225,985 (GRCm39) unclassified probably benign
R4327:C9orf72 UTSW 4 35,225,985 (GRCm39) unclassified probably benign
R4328:C9orf72 UTSW 4 35,225,985 (GRCm39) unclassified probably benign
R4844:C9orf72 UTSW 4 35,213,565 (GRCm39) missense possibly damaging 0.47
R5150:C9orf72 UTSW 4 35,193,270 (GRCm39) missense possibly damaging 0.92
R5528:C9orf72 UTSW 4 35,213,556 (GRCm39) missense probably benign 0.18
R5789:C9orf72 UTSW 4 35,226,112 (GRCm39) unclassified probably benign
R7790:C9orf72 UTSW 4 35,192,997 (GRCm39) missense unknown
R7805:C9orf72 UTSW 4 35,194,170 (GRCm39) missense
R8115:C9orf72 UTSW 4 35,218,763 (GRCm39) missense
R9049:C9orf72 UTSW 4 35,192,964 (GRCm39) missense unknown
R9327:C9orf72 UTSW 4 35,205,883 (GRCm39) missense
R9373:C9orf72 UTSW 4 35,196,985 (GRCm39) missense
R9590:C9orf72 UTSW 4 35,218,557 (GRCm39) missense
R9591:C9orf72 UTSW 4 35,218,557 (GRCm39) missense
Predicted Primers PCR Primer
(F):5'- AGGAGTTCACCTCGAAGGAG -3'
(R):5'- GCGGCTCTTGGAAGAAAAGC -3'

Sequencing Primer
(F):5'- GCGTCTCACTCACCCACTCG -3'
(R):5'- ACTGGCATCTCAAGGCTGG -3'
Posted On 2015-10-08