Incidental Mutation 'R2173:Pomt1'
ID 237596
Institutional Source Beutler Lab
Gene Symbol Pomt1
Ensembl Gene ENSMUSG00000039254
Gene Name protein-O-mannosyltransferase 1
Synonyms
MMRRC Submission 040175-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.134) question?
Stock # R2173 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 32126652-32145017 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 32140912 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 515 (Y515H)
Ref Sequence ENSEMBL: ENSMUSP00000038722 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000002625] [ENSMUST00000036473]
AlphaFold Q8R2R1
Predicted Effect probably benign
Transcript: ENSMUST00000002625
SMART Domains Protein: ENSMUSP00000002625
Gene: ENSMUSG00000002550

DomainStartEndE-ValueType
low complexity region 8 19 N/A INTRINSIC
Pfam:CoaE 30 198 1.1e-8 PFAM
Pfam:AAA_17 31 188 3.8e-8 PFAM
Pfam:PRK 31 225 1.9e-53 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000036473
AA Change: Y515H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000038722
Gene: ENSMUSG00000039254
AA Change: Y515H

DomainStartEndE-ValueType
Pfam:PMT 42 289 2.8e-96 PFAM
MIR 318 381 7.45e-8 SMART
MIR 392 449 1.65e-9 SMART
MIR 456 513 6.2e-5 SMART
Pfam:PMT_4TMC 542 740 3.9e-50 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129163
Predicted Effect probably benign
Transcript: ENSMUST00000132516
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132853
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133804
Predicted Effect noncoding transcript
Transcript: ENSMUST00000138000
Predicted Effect noncoding transcript
Transcript: ENSMUST00000151598
Predicted Effect probably benign
Transcript: ENSMUST00000192998
Meta Mutation Damage Score 0.3421 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.6%
Validation Efficiency 97% (66/68)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is an O-mannosyltransferase that requires interaction with the product of the POMT2 gene for enzymatic function. The encoded protein is found in the membrane of the endoplasmic reticulum. Defects in this gene are a cause of Walker-Warburg syndrome (WWS) and limb-girdle muscular dystrophy type 2K (LGMD2K). Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2008]
PHENOTYPE: Homozygous mutation of this gene with one allele results in embryonic lethality with disruption of Reichert's membrane. Heterozygous mutation with a second allele results in ectasia in kidney and liver veins and an increased neutrophil count. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Alpk1 T A 3: 127,477,239 (GRCm39) H273L probably damaging Het
Alpk3 A G 7: 80,726,648 (GRCm39) Y111C probably damaging Het
Anapc2 T G 2: 25,163,288 (GRCm39) V175G probably benign Het
Arhgap30 T C 1: 171,235,335 (GRCm39) S570P probably damaging Het
AU040320 T C 4: 126,686,069 (GRCm39) L215P probably benign Het
Ccdc59 A T 10: 105,677,388 (GRCm39) K9M possibly damaging Het
Ccdc65 A G 15: 98,618,914 (GRCm39) N298D probably benign Het
Cfap70 T A 14: 20,458,630 (GRCm39) N727Y probably benign Het
Clcn7 A G 17: 25,364,583 (GRCm39) H63R probably benign Het
Corin A T 5: 72,661,422 (GRCm39) C24S probably benign Het
Cyp1a2 A G 9: 57,584,798 (GRCm39) W419R probably damaging Het
Dlgap4 C A 2: 156,604,732 (GRCm39) A256D probably damaging Het
Eif4enif1 A G 11: 3,192,367 (GRCm39) probably null Het
Eri2 A G 7: 119,385,766 (GRCm39) V245A possibly damaging Het
Erich6b T C 14: 75,896,332 (GRCm39) F73L probably benign Het
Fam110a A G 2: 151,812,429 (GRCm39) C114R probably damaging Het
Fam149a T C 8: 45,806,991 (GRCm39) D288G probably damaging Het
Fam171a1 T A 2: 3,226,656 (GRCm39) Y596* probably null Het
Fsd1 A G 17: 56,298,223 (GRCm39) T183A possibly damaging Het
Fut10 T A 8: 31,726,159 (GRCm39) Y305N probably damaging Het
Ganab A T 19: 8,879,624 (GRCm39) probably benign Het
Gm9922 G T 14: 101,967,012 (GRCm39) probably benign Het
Gp9 A G 6: 87,756,035 (GRCm39) T17A probably benign Het
Gxylt2 T C 6: 100,775,115 (GRCm39) Y345H probably damaging Het
Herc2 A G 7: 55,835,699 (GRCm39) H3269R probably benign Het
Hpx A T 7: 105,241,290 (GRCm39) S374T probably benign Het
Hspa5 T C 2: 34,664,674 (GRCm39) V376A probably damaging Het
Hyi T C 4: 118,219,381 (GRCm39) probably benign Het
Impdh2 G A 9: 108,442,593 (GRCm39) probably null Het
Kremen2 A C 17: 23,961,770 (GRCm39) W246G probably damaging Het
Krt87 A G 15: 101,385,818 (GRCm39) V259A probably damaging Het
L3mbtl4 A T 17: 68,894,188 (GRCm39) H398L probably damaging Het
Lama5 C A 2: 179,838,035 (GRCm39) V894L probably benign Het
Maml2 A G 9: 13,532,912 (GRCm39) probably benign Het
Nup153 A T 13: 46,855,076 (GRCm39) probably benign Het
Or10g6 T G 9: 39,934,550 (GRCm39) I287S probably damaging Het
Or2y15 G T 11: 49,350,967 (GRCm39) V154L probably benign Het
Or5k14 A G 16: 58,692,982 (GRCm39) F177S probably damaging Het
Or8b3b T C 9: 38,584,240 (GRCm39) I180V probably benign Het
Or9r7 G A 10: 129,962,372 (GRCm39) P185S probably benign Het
Otof C T 5: 30,543,718 (GRCm39) R582H probably damaging Het
Otud4 T C 8: 80,395,093 (GRCm39) S543P probably damaging Het
Pde6a A G 18: 61,387,453 (GRCm39) D448G probably damaging Het
Phgdh A G 3: 98,222,427 (GRCm39) V388A probably benign Het
Plin3 G T 17: 56,586,891 (GRCm39) D385E possibly damaging Het
Polg G T 7: 79,105,341 (GRCm39) D734E probably damaging Het
Prr35 A C 17: 26,167,461 (GRCm39) H25Q probably damaging Het
Pwwp2a G A 11: 43,573,313 (GRCm39) A132T probably benign Het
Rbm6 A T 9: 107,729,390 (GRCm39) F419L possibly damaging Het
Rfx5 A G 3: 94,864,027 (GRCm39) probably null Het
Rnf135 G A 11: 80,080,066 (GRCm39) S119N probably benign Het
Scfd1 T A 12: 51,433,862 (GRCm39) D51E probably benign Het
Smox A T 2: 131,353,944 (GRCm39) E5D possibly damaging Het
Srpk2 T C 5: 23,723,613 (GRCm39) probably null Het
Syne2 T A 12: 76,147,763 (GRCm39) probably benign Het
Tcf20 A G 15: 82,738,893 (GRCm39) S853P possibly damaging Het
Tmem131l A G 3: 83,833,452 (GRCm39) F804L probably damaging Het
Ttll8 A G 15: 88,798,800 (GRCm39) L645P probably damaging Het
Ubr3 T A 2: 69,727,743 (GRCm39) H35Q probably benign Het
Uck1 GCCAACACC GCC 2: 32,146,088 (GRCm39) probably benign Het
Vmn2r70 A T 7: 85,214,290 (GRCm39) H287Q probably benign Het
Vps26a A T 10: 62,304,171 (GRCm39) I150N probably damaging Het
Zfp605 G A 5: 110,275,323 (GRCm39) R147H probably benign Het
Zfyve16 A G 13: 92,631,596 (GRCm39) M1333T probably damaging Het
Other mutations in Pomt1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00093:Pomt1 APN 2 32,131,784 (GRCm39) missense probably benign
IGL01926:Pomt1 APN 2 32,133,484 (GRCm39) missense probably benign 0.23
IGL02237:Pomt1 APN 2 32,135,689 (GRCm39) missense probably benign 0.18
IGL02281:Pomt1 APN 2 32,138,658 (GRCm39) missense possibly damaging 0.95
IGL03001:Pomt1 APN 2 32,134,338 (GRCm39) missense probably benign
IGL03216:Pomt1 APN 2 32,132,955 (GRCm39) missense probably damaging 0.99
IGL03343:Pomt1 APN 2 32,143,724 (GRCm39) splice site probably benign
R0049:Pomt1 UTSW 2 32,142,023 (GRCm39) missense possibly damaging 0.88
R0049:Pomt1 UTSW 2 32,142,023 (GRCm39) missense possibly damaging 0.88
R0975:Pomt1 UTSW 2 32,143,907 (GRCm39) critical splice donor site probably null
R1199:Pomt1 UTSW 2 32,140,504 (GRCm39) missense probably benign
R1414:Pomt1 UTSW 2 32,133,622 (GRCm39) splice site probably benign
R1421:Pomt1 UTSW 2 32,126,765 (GRCm39) unclassified probably benign
R1806:Pomt1 UTSW 2 32,131,680 (GRCm39) missense probably damaging 1.00
R2209:Pomt1 UTSW 2 32,140,874 (GRCm39) missense possibly damaging 0.90
R2302:Pomt1 UTSW 2 32,133,671 (GRCm39) missense probably benign 0.00
R3084:Pomt1 UTSW 2 32,134,252 (GRCm39) missense probably benign 0.02
R3774:Pomt1 UTSW 2 32,134,262 (GRCm39) missense possibly damaging 0.93
R3933:Pomt1 UTSW 2 32,135,631 (GRCm39) missense probably benign 0.00
R4177:Pomt1 UTSW 2 32,138,689 (GRCm39) missense probably damaging 0.99
R4626:Pomt1 UTSW 2 32,144,424 (GRCm39) missense possibly damaging 0.84
R4645:Pomt1 UTSW 2 32,132,888 (GRCm39) intron probably benign
R4864:Pomt1 UTSW 2 32,142,004 (GRCm39) missense probably benign 0.02
R4911:Pomt1 UTSW 2 32,131,691 (GRCm39) missense probably damaging 0.97
R5143:Pomt1 UTSW 2 32,144,341 (GRCm39) missense probably benign 0.23
R5288:Pomt1 UTSW 2 32,134,311 (GRCm39) nonsense probably null
R5385:Pomt1 UTSW 2 32,134,311 (GRCm39) nonsense probably null
R5718:Pomt1 UTSW 2 32,138,704 (GRCm39) missense possibly damaging 0.91
R5735:Pomt1 UTSW 2 32,133,517 (GRCm39) missense probably damaging 1.00
R5754:Pomt1 UTSW 2 32,137,602 (GRCm39) missense probably damaging 0.99
R5817:Pomt1 UTSW 2 32,138,691 (GRCm39) missense probably damaging 0.97
R6304:Pomt1 UTSW 2 32,140,802 (GRCm39) missense probably damaging 1.00
R6477:Pomt1 UTSW 2 32,138,728 (GRCm39) splice site probably null
R6793:Pomt1 UTSW 2 32,132,961 (GRCm39) missense probably damaging 1.00
R6918:Pomt1 UTSW 2 32,142,873 (GRCm39) splice site probably null
R7114:Pomt1 UTSW 2 32,143,848 (GRCm39) missense probably benign 0.41
R8140:Pomt1 UTSW 2 32,134,309 (GRCm39) missense probably damaging 1.00
R8380:Pomt1 UTSW 2 32,135,619 (GRCm39) missense probably damaging 1.00
R9082:Pomt1 UTSW 2 32,142,973 (GRCm39) missense probably damaging 0.98
R9578:Pomt1 UTSW 2 32,133,543 (GRCm39) critical splice donor site probably null
Z1177:Pomt1 UTSW 2 32,127,101 (GRCm39) start gained probably benign
Predicted Primers PCR Primer
(F):5'- CTGTTTTATAGTACACGCAGGGG -3'
(R):5'- AGCACAAACGCCTTATTACTCATG -3'

Sequencing Primer
(F):5'- AGGGACCTGCTGACACAG -3'
(R):5'- CAAACGCCTTATTACTCATGGATGGG -3'
Posted On 2014-10-02