Incidental Mutation 'R5840:Chmp1a'
ID 450382
Institutional Source Beutler Lab
Gene Symbol Chmp1a
Ensembl Gene ENSMUSG00000000743
Gene Name charged multivesicular body protein 1A
Synonyms Pcoln3, chromatin modifying protein 1A, 2900018H07Rik
MMRRC Submission 044060-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.374) question?
Stock # R5840 (G1)
Quality Score 225
Status Validated
Chromosome 8
Chromosomal Location 123931003-123939502 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 123934839 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Arginine at position 39 (Q39R)
Ref Sequence ENSEMBL: ENSMUSP00000000759 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000000759] [ENSMUST00000060133] [ENSMUST00000127664] [ENSMUST00000212637] [ENSMUST00000212346] [ENSMUST00000212161] [ENSMUST00000212523] [ENSMUST00000212760] [ENSMUST00000212892]
AlphaFold Q921W0
Predicted Effect probably benign
Transcript: ENSMUST00000000759
AA Change: Q39R

PolyPhen 2 Score 0.224 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000000759
Gene: ENSMUSG00000000743
AA Change: Q39R

DomainStartEndE-ValueType
Pfam:Snf7 4 174 6.4e-15 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000060133
SMART Domains Protein: ENSMUSP00000058002
Gene: ENSMUSG00000048478

DomainStartEndE-ValueType
low complexity region 4 28 N/A INTRINSIC
Pfam:DUF4609 63 130 3.4e-42 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000127664
SMART Domains Protein: ENSMUSP00000118564
Gene: ENSMUSG00000092329

DomainStartEndE-ValueType
Pfam:Glycos_transf_2 104 287 7.4e-31 PFAM
Pfam:Glyco_transf_7C 261 331 4.9e-8 PFAM
RICIN 406 531 9.28e-27 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000139165
Predicted Effect noncoding transcript
Transcript: ENSMUST00000167655
Predicted Effect noncoding transcript
Transcript: ENSMUST00000172336
Predicted Effect noncoding transcript
Transcript: ENSMUST00000212107
Predicted Effect probably benign
Transcript: ENSMUST00000212637
Predicted Effect probably benign
Transcript: ENSMUST00000212346
Predicted Effect probably benign
Transcript: ENSMUST00000212161
Predicted Effect probably benign
Transcript: ENSMUST00000212523
Predicted Effect probably benign
Transcript: ENSMUST00000212760
Predicted Effect probably benign
Transcript: ENSMUST00000212892
Meta Mutation Damage Score 0.1774 question?
Coding Region Coverage
  • 1x: 99.8%
  • 3x: 99.3%
  • 10x: 96.5%
  • 20x: 88.1%
Validation Efficiency 99% (75/76)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the CHMP/Chmp family of proteins which are involved in multivesicular body sorting of proteins to the interiors of lysosomes. The initial prediction of the protein sequence encoded by this gene suggested that the encoded protein was a metallopeptidase. The nomenclature has been updated recently to reflect the correct biological function of this encoded protein. Several transcripts encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]
Allele List at MGI
Other mutations in this stock
Total: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca2 G A 2: 25,323,371 (GRCm39) R113Q probably benign Het
Aip G A 19: 4,166,010 (GRCm39) P147L possibly damaging Het
Anapc1 A C 2: 128,448,957 (GRCm39) probably benign Het
Arhgap42 C T 9: 9,046,518 (GRCm39) V240I possibly damaging Het
Axdnd1 T C 1: 156,176,528 (GRCm39) E684G probably damaging Het
BC005624 G A 2: 30,871,869 (GRCm39) R2W probably benign Het
Cd177 T G 7: 24,457,495 (GRCm39) Q182P probably damaging Het
Cdca5 G A 19: 6,140,399 (GRCm39) E187K possibly damaging Het
Dab2ip A G 2: 35,617,511 (GRCm39) I1079V probably damaging Het
Dip2c A T 13: 9,556,712 (GRCm39) E85D possibly damaging Het
Elmo2 A T 2: 165,137,472 (GRCm39) S497R possibly damaging Het
Ephb6 C T 6: 41,592,507 (GRCm39) A339V possibly damaging Het
Foxred1 T C 9: 35,121,435 (GRCm39) K38E probably damaging Het
Frem2 T A 3: 53,555,342 (GRCm39) T1732S probably damaging Het
Fto A G 8: 92,393,068 (GRCm39) probably benign Het
Gm17430 T A 18: 9,726,528 (GRCm39) Q48L probably damaging Het
Gng2 A G 14: 19,925,882 (GRCm39) I70T probably damaging Het
Gtf2a2 A G 9: 69,922,575 (GRCm39) probably benign Het
Invs A G 4: 48,396,284 (GRCm39) D263G probably damaging Het
Itga2b C T 11: 102,352,157 (GRCm39) V475M probably damaging Het
Kansl1l A G 1: 66,809,374 (GRCm39) probably benign Het
Klhl25 T C 7: 75,516,440 (GRCm39) F449L possibly damaging Het
Lamb1 T A 12: 31,316,755 (GRCm39) C83S probably damaging Het
Loxl4 G T 19: 42,587,154 (GRCm39) T648K probably damaging Het
Lrit2 T C 14: 36,790,962 (GRCm39) F214L possibly damaging Het
N4bp2 T G 5: 65,965,437 (GRCm39) L1162R probably damaging Het
Naa40 A T 19: 7,207,373 (GRCm39) I117N probably benign Het
Ncapd3 T C 9: 27,006,054 (GRCm39) S1492P probably benign Het
Nf2 T A 11: 4,766,146 (GRCm39) D128V probably benign Het
Nox4 T C 7: 87,010,001 (GRCm39) S401P probably benign Het
Nt5c1b T C 12: 10,427,171 (GRCm39) V323A probably damaging Het
Or52a33 C T 7: 103,288,463 (GRCm39) V295I probably benign Het
Or52s19 T A 7: 103,007,576 (GRCm39) H275L probably damaging Het
Or5b118 G A 19: 13,449,242 (GRCm39) V303I probably benign Het
Pcdhb14 T C 18: 37,581,803 (GRCm39) V303A probably benign Het
Pde8a C A 7: 80,863,713 (GRCm39) H17Q probably benign Het
Pfkl C T 10: 77,824,558 (GRCm39) V716I probably benign Het
Phc3 G A 3: 30,990,732 (GRCm39) S495L possibly damaging Het
Psg18 A G 7: 18,080,527 (GRCm39) probably benign Het
Rcc2 T G 4: 140,439,449 (GRCm39) N175K possibly damaging Het
Rhot2 G A 17: 26,059,032 (GRCm39) T276I probably benign Het
Rnase9 A T 14: 51,276,445 (GRCm39) Y178N probably benign Het
Sema4b T C 7: 79,868,697 (GRCm39) C297R probably damaging Het
Slc35d2 T C 13: 64,266,227 (GRCm39) probably null Het
Sptlc3 A T 2: 139,389,126 (GRCm39) N169Y probably damaging Het
Srsf9 T G 5: 115,469,524 (GRCm39) M29R probably benign Het
Stip1 C A 19: 6,999,436 (GRCm39) D449Y possibly damaging Het
Syne2 T A 12: 75,927,065 (GRCm39) probably null Het
Tgm5 A G 2: 120,916,141 (GRCm39) probably null Het
Thbs2 A T 17: 14,901,692 (GRCm39) probably null Het
Trak2 T C 1: 58,958,432 (GRCm39) E283G probably damaging Het
Trbv21 A G 6: 41,179,792 (GRCm39) Y36C probably damaging Het
Trpm7 A T 2: 126,664,531 (GRCm39) Y949* probably null Het
Ubqln5 T C 7: 103,778,161 (GRCm39) D221G possibly damaging Het
Ubxn4 T A 1: 128,187,262 (GRCm39) V85D possibly damaging Het
Vmn1r172 T A 7: 23,359,600 (GRCm39) W162R probably benign Het
Vrk2 A G 11: 26,484,314 (GRCm39) probably benign Het
Zc3h8 A C 2: 128,771,824 (GRCm39) D276E probably benign Het
Zfp369 C T 13: 65,445,092 (GRCm39) T745I possibly damaging Het
Zfp608 T C 18: 55,031,978 (GRCm39) K654R probably damaging Het
Other mutations in Chmp1a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00089:Chmp1a APN 8 123,935,758 (GRCm39) critical splice donor site probably null
IGL01872:Chmp1a APN 8 123,932,976 (GRCm39) missense probably damaging 1.00
IGL02964:Chmp1a APN 8 123,934,806 (GRCm39) missense probably damaging 0.98
R0288:Chmp1a UTSW 8 123,934,745 (GRCm39) missense probably damaging 1.00
R2074:Chmp1a UTSW 8 123,934,761 (GRCm39) missense probably damaging 0.98
R2075:Chmp1a UTSW 8 123,934,761 (GRCm39) missense probably damaging 0.98
R5070:Chmp1a UTSW 8 123,933,054 (GRCm39) missense probably benign 0.13
R8307:Chmp1a UTSW 8 123,932,980 (GRCm39) missense probably damaging 0.98
Z1177:Chmp1a UTSW 8 123,933,070 (GRCm39) missense probably benign 0.05
Predicted Primers PCR Primer
(F):5'- TCTAGAAAGGCACCAGGTCC -3'
(R):5'- AGATGTGGCTCTGGAGGAAC -3'

Sequencing Primer
(F):5'- GGTCCTGCCACTAAACCCTAC -3'
(R):5'- AGCAGACTGGACCCCTAG -3'
Posted On 2016-12-20