Incidental Mutation 'R4167:Man2c1'
ID 320625
Institutional Source Beutler Lab
Gene Symbol Man2c1
Ensembl Gene ENSMUSG00000032295
Gene Name mannosidase, alpha, class 2C, member 1
Synonyms 1110025H24Rik
MMRRC Submission 041008-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4167 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 57037953-57049497 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 57045310 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 473 (D473G)
Ref Sequence ENSEMBL: ENSMUSP00000034836 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034836] [ENSMUST00000159130] [ENSMUST00000161182] [ENSMUST00000160147] [ENSMUST00000161663] [ENSMUST00000161393] [ENSMUST00000160584] [ENSMUST00000161338] [ENSMUST00000162915] [ENSMUST00000190245]
AlphaFold Q91W89
Predicted Effect probably benign
Transcript: ENSMUST00000034836
AA Change: D473G

PolyPhen 2 Score 0.150 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000034836
Gene: ENSMUSG00000032295
AA Change: D473G

DomainStartEndE-ValueType
low complexity region 187 195 N/A INTRINSIC
Pfam:Glyco_hydro_38 251 510 4.3e-89 PFAM
Alpha-mann_mid 516 593 1.37e-26 SMART
low complexity region 603 613 N/A INTRINSIC
Pfam:Glyco_hydro_38C 619 1029 1.3e-84 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000159101
SMART Domains Protein: ENSMUSP00000124304
Gene: ENSMUSG00000032295

DomainStartEndE-ValueType
Alpha-mann_mid 21 100 1.22e-32 SMART
low complexity region 110 120 N/A INTRINSIC
low complexity region 164 180 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000159130
Predicted Effect noncoding transcript
Transcript: ENSMUST00000159402
Predicted Effect noncoding transcript
Transcript: ENSMUST00000159496
Predicted Effect noncoding transcript
Transcript: ENSMUST00000159711
Predicted Effect probably benign
Transcript: ENSMUST00000161182
AA Change: D374G

PolyPhen 2 Score 0.033 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000124020
Gene: ENSMUSG00000032295
AA Change: D374G

DomainStartEndE-ValueType
Pfam:Glyco_hydro_38 175 411 9.4e-67 PFAM
Alpha-mann_mid 417 496 1.22e-32 SMART
low complexity region 506 516 N/A INTRINSIC
Pfam:Glyco_hydro_38C 522 932 1.1e-84 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000160147
AA Change: D473G

PolyPhen 2 Score 0.042 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000125478
Gene: ENSMUSG00000032295
AA Change: D473G

DomainStartEndE-ValueType
low complexity region 187 195 N/A INTRINSIC
Pfam:Glyco_hydro_38 251 510 2.8e-86 PFAM
Alpha-mann_mid 516 595 1.22e-32 SMART
low complexity region 605 615 N/A INTRINSIC
Pfam:Glyco_hydro_38C 621 1031 1.2e-84 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000161663
AA Change: D514G

PolyPhen 2 Score 0.058 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000124124
Gene: ENSMUSG00000032295
AA Change: D514G

DomainStartEndE-ValueType
low complexity region 187 195 N/A INTRINSIC
Pfam:Glyco_hydro_38 302 551 1.8e-81 PFAM
Alpha-mann_mid 557 636 1.22e-32 SMART
low complexity region 646 656 N/A INTRINSIC
Pfam:Glyco_hydro_38C 662 866 1.2e-25 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000159843
Predicted Effect noncoding transcript
Transcript: ENSMUST00000159954
Predicted Effect noncoding transcript
Transcript: ENSMUST00000160042
Predicted Effect noncoding transcript
Transcript: ENSMUST00000160280
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161696
Predicted Effect probably benign
Transcript: ENSMUST00000160426
SMART Domains Protein: ENSMUSP00000124005
Gene: ENSMUSG00000032295

DomainStartEndE-ValueType
Alpha-mann_mid 24 77 4.48e-1 SMART
low complexity region 87 97 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000161393
Predicted Effect probably benign
Transcript: ENSMUST00000160584
SMART Domains Protein: ENSMUSP00000123840
Gene: ENSMUSG00000032295

DomainStartEndE-ValueType
low complexity region 187 195 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000161338
Predicted Effect noncoding transcript
Transcript: ENSMUST00000162634
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161875
Predicted Effect noncoding transcript
Transcript: ENSMUST00000162340
Predicted Effect probably benign
Transcript: ENSMUST00000162915
Predicted Effect probably benign
Transcript: ENSMUST00000190245
SMART Domains Protein: ENSMUSP00000139917
Gene: ENSMUSG00000032298

DomainStartEndE-ValueType
Fapy_DNA_glyco 2 124 2.9e-16 SMART
H2TH 139 224 9.35e-2 SMART
Pfam:Neil1-DNA_bind 252 290 2.1e-29 PFAM
Meta Mutation Damage Score 0.7288 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.5%
  • 20x: 96.0%
Validation Efficiency 94% (31/33)
MGI Phenotype PHENOTYPE: Germ line null mutants display neuronal and glia degeneration, glycogen accumulation, and liver and kidney damage. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 29 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Casp6 A G 3: 129,706,993 (GRCm39) H201R probably damaging Het
Cd200r3 T A 16: 44,774,552 (GRCm39) D188E probably benign Het
Cdh16 A G 8: 105,344,362 (GRCm39) L59P probably benign Het
Dcp2 T A 18: 44,529,034 (GRCm39) Y50N probably damaging Het
Elk3 A G 10: 93,101,197 (GRCm39) probably null Het
Fam78b T C 1: 166,829,301 (GRCm39) V51A possibly damaging Het
Gabrb2 A T 11: 42,312,155 (GRCm39) probably benign Het
Glyctk G T 9: 106,034,961 (GRCm39) A35E probably benign Het
Kat14 A G 2: 144,236,030 (GRCm39) E254G probably damaging Het
Kcng1 T A 2: 168,104,617 (GRCm39) S410C probably damaging Het
Krt74 A G 15: 101,667,304 (GRCm39) noncoding transcript Het
Lrp12 T C 15: 39,748,409 (GRCm39) T70A probably damaging Het
Mindy4 G A 6: 55,201,331 (GRCm39) G339S possibly damaging Het
Naip1 C T 13: 100,580,794 (GRCm39) G151D probably benign Het
Ndufaf7 G A 17: 79,252,415 (GRCm39) V275I probably benign Het
Nppb T A 4: 148,071,431 (GRCm39) L121* probably null Het
Oog2 A T 4: 143,922,782 (GRCm39) Q349L probably benign Het
Or5d39 T C 2: 87,980,189 (GRCm39) H58R probably damaging Het
Or5v1b T C 17: 37,840,897 (GRCm39) S10P possibly damaging Het
Pcdhgb8 T G 18: 37,895,596 (GRCm39) V222G possibly damaging Het
Plcd3 A T 11: 102,969,290 (GRCm39) C226S probably damaging Het
Plxdc2 A G 2: 16,570,196 (GRCm39) E125G probably damaging Het
Rnf213 A G 11: 119,332,069 (GRCm39) E2426G probably damaging Het
Rraga T C 4: 86,494,304 (GRCm39) V50A possibly damaging Het
Scmh1 T C 4: 120,386,473 (GRCm39) probably benign Het
Slc9a9 A G 9: 95,110,952 (GRCm39) Y590C probably damaging Het
Snx20 C T 8: 89,354,013 (GRCm39) R239Q probably benign Het
Vmn2r59 A G 7: 41,670,732 (GRCm39) probably benign Het
Zfp128 A G 7: 12,624,289 (GRCm39) D219G probably benign Het
Other mutations in Man2c1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01314:Man2c1 APN 9 57,049,103 (GRCm39) missense probably benign
IGL01408:Man2c1 APN 9 57,048,884 (GRCm39) missense probably damaging 1.00
IGL01618:Man2c1 APN 9 57,048,840 (GRCm39) unclassified probably benign
IGL01750:Man2c1 APN 9 57,048,064 (GRCm39) critical splice donor site probably null
IGL01796:Man2c1 APN 9 57,045,244 (GRCm39) missense possibly damaging 0.52
IGL02661:Man2c1 APN 9 57,044,766 (GRCm39) missense probably damaging 1.00
IGL03166:Man2c1 APN 9 57,046,382 (GRCm39) missense probably damaging 1.00
IGL03176:Man2c1 APN 9 57,048,030 (GRCm39) missense probably benign 0.05
IGL03209:Man2c1 APN 9 57,049,114 (GRCm39) missense probably benign 0.00
R0014:Man2c1 UTSW 9 57,046,985 (GRCm39) missense probably benign 0.00
R0329:Man2c1 UTSW 9 57,048,467 (GRCm39) missense probably benign 0.40
R0432:Man2c1 UTSW 9 57,042,881 (GRCm39) missense probably damaging 1.00
R1448:Man2c1 UTSW 9 57,042,503 (GRCm39) missense probably benign 0.23
R1616:Man2c1 UTSW 9 57,042,793 (GRCm39) missense probably benign 0.00
R1838:Man2c1 UTSW 9 57,044,621 (GRCm39) missense probably benign 0.07
R2511:Man2c1 UTSW 9 57,048,672 (GRCm39) splice site probably null
R3751:Man2c1 UTSW 9 57,048,058 (GRCm39) missense probably damaging 1.00
R3771:Man2c1 UTSW 9 57,047,661 (GRCm39) unclassified probably benign
R3772:Man2c1 UTSW 9 57,047,661 (GRCm39) unclassified probably benign
R4110:Man2c1 UTSW 9 57,044,055 (GRCm39) missense probably damaging 0.98
R4116:Man2c1 UTSW 9 57,047,589 (GRCm39) critical splice donor site probably null
R4169:Man2c1 UTSW 9 57,045,310 (GRCm39) missense probably benign 0.15
R4170:Man2c1 UTSW 9 57,045,310 (GRCm39) missense probably benign 0.15
R4405:Man2c1 UTSW 9 57,046,367 (GRCm39) missense probably damaging 0.98
R4551:Man2c1 UTSW 9 57,038,445 (GRCm39) missense probably damaging 1.00
R4618:Man2c1 UTSW 9 57,049,439 (GRCm39) splice site probably null
R4798:Man2c1 UTSW 9 57,048,469 (GRCm39) nonsense probably null
R4903:Man2c1 UTSW 9 57,046,240 (GRCm39) missense probably benign 0.08
R5030:Man2c1 UTSW 9 57,047,923 (GRCm39) missense probably benign 0.00
R5079:Man2c1 UTSW 9 57,044,000 (GRCm39) missense probably damaging 1.00
R5086:Man2c1 UTSW 9 57,038,924 (GRCm39) missense probably damaging 0.96
R6430:Man2c1 UTSW 9 57,038,517 (GRCm39) missense possibly damaging 0.91
R6695:Man2c1 UTSW 9 57,048,875 (GRCm39) missense probably benign 0.03
R6743:Man2c1 UTSW 9 57,042,849 (GRCm39) missense probably benign 0.41
R7011:Man2c1 UTSW 9 57,045,117 (GRCm39) missense probably damaging 1.00
R7493:Man2c1 UTSW 9 57,048,412 (GRCm39) missense probably damaging 0.98
R7513:Man2c1 UTSW 9 57,046,683 (GRCm39) missense probably benign 0.44
R7527:Man2c1 UTSW 9 57,045,100 (GRCm39) nonsense probably null
R7540:Man2c1 UTSW 9 57,047,559 (GRCm39) missense probably damaging 1.00
R7760:Man2c1 UTSW 9 57,046,647 (GRCm39) missense probably benign 0.23
R7868:Man2c1 UTSW 9 57,045,270 (GRCm39) missense probably damaging 0.99
R8261:Man2c1 UTSW 9 57,046,942 (GRCm39) missense probably benign 0.17
R8397:Man2c1 UTSW 9 57,042,783 (GRCm39) missense probably benign 0.01
R8429:Man2c1 UTSW 9 57,038,445 (GRCm39) missense probably damaging 1.00
R8519:Man2c1 UTSW 9 57,044,061 (GRCm39) missense probably benign 0.12
R8530:Man2c1 UTSW 9 57,038,922 (GRCm39) missense probably damaging 1.00
R8544:Man2c1 UTSW 9 57,038,325 (GRCm39) splice site probably null
R8925:Man2c1 UTSW 9 57,048,456 (GRCm39) nonsense probably null
R8927:Man2c1 UTSW 9 57,048,456 (GRCm39) nonsense probably null
R8960:Man2c1 UTSW 9 57,045,279 (GRCm39) missense probably damaging 1.00
R9171:Man2c1 UTSW 9 57,044,317 (GRCm39) nonsense probably null
R9326:Man2c1 UTSW 9 57,042,904 (GRCm39) missense probably damaging 1.00
R9414:Man2c1 UTSW 9 57,044,030 (GRCm39) missense possibly damaging 0.95
Predicted Primers PCR Primer
(F):5'- TCATATGGAATGCAGGGCAGTG -3'
(R):5'- CCTGCACCATATCCTCAAGGTAG -3'

Sequencing Primer
(F):5'- GGGGACACGGGATGCTG -3'
(R):5'- CCATATCCTCAAGGTAGAAGTTTGG -3'
Posted On 2015-06-12