Incidental Mutation 'R2127:Rtca'
ID 227593
Institutional Source Beutler Lab
Gene Symbol Rtca
Ensembl Gene ENSMUSG00000000339
Gene Name RNA 3'-terminal phosphate cyclase
Synonyms Rtcd1, 2310009A18Rik
MMRRC Submission 040130-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.149) question?
Stock # R2127 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 116282612-116301852 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 116291323 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Leucine at position 219 (R219L)
Ref Sequence ENSEMBL: ENSMUSP00000000348 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000000348] [ENSMUST00000140677] [ENSMUST00000143425] [ENSMUST00000153005]
AlphaFold Q9D7H3
Predicted Effect possibly damaging
Transcript: ENSMUST00000000348
AA Change: R219L

PolyPhen 2 Score 0.845 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000000348
Gene: ENSMUSG00000000339
AA Change: R219L

DomainStartEndE-ValueType
Pfam:RTC 12 338 4.3e-89 PFAM
Pfam:RTC_insert 185 287 4.5e-23 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124486
Predicted Effect probably benign
Transcript: ENSMUST00000140677
SMART Domains Protein: ENSMUSP00000117610
Gene: ENSMUSG00000000339

DomainStartEndE-ValueType
Pfam:RTC 8 51 3.2e-17 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000143425
SMART Domains Protein: ENSMUSP00000121357
Gene: ENSMUSG00000000339

DomainStartEndE-ValueType
Pfam:RTC 8 102 9.8e-37 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000153005
AA Change: R113L

PolyPhen 2 Score 0.209 (Sensitivity: 0.92; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000119463
Gene: ENSMUSG00000000339
AA Change: R113L

DomainStartEndE-ValueType
Pfam:RTC 1 133 1.1e-27 PFAM
Pfam:RTC_insert 78 142 2e-14 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000180969
Meta Mutation Damage Score 0.1795 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.9%
Validation Efficiency 98% (93/95)
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 RNA 3'-phosphate cyclase family. The encoded protein plays a role in RNA metabolism by catalyzing the ATP-dependent conversion of the 3'-phosphate of RNA substrates to a 2',3'-cyclic phosphodiester. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]
PHENOTYPE: Mice homozygous for a hypomorphic allele exhibit incomplete prenatal lethality and enhanced retinal ganglion cell axon regeneration after optic nerve crush injury. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 93 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930449I24Rik T A 5: 146,441,752 (GRCm39) S300T possibly damaging Het
A2ml1 A C 6: 128,535,400 (GRCm39) V770G probably damaging Het
Abca6 A G 11: 110,110,475 (GRCm39) I558T probably benign Het
Abhd17c C A 7: 83,759,870 (GRCm39) G295W probably damaging Het
Actn3 G A 19: 4,921,703 (GRCm39) A159V probably damaging Het
Adgrv1 A T 13: 81,705,199 (GRCm39) F1537Y probably damaging Het
Agbl1 G T 7: 76,069,628 (GRCm39) V373F possibly damaging Het
Aldh1a1 A T 19: 20,620,279 (GRCm39) E485D probably benign Het
Amdhd2 A G 17: 24,377,282 (GRCm39) probably null Het
Armc3 A G 2: 19,206,622 (GRCm39) D15G probably damaging Het
Atp2b2 A G 6: 113,737,611 (GRCm39) L921P probably damaging Het
Btbd16 A G 7: 130,386,038 (GRCm39) N88S probably benign Het
Capn10 T A 1: 92,865,756 (GRCm39) C77* probably null Het
Caskin1 T C 17: 24,715,970 (GRCm39) probably null Het
Catsper4 T C 4: 133,941,117 (GRCm39) D254G probably benign Het
Catsperg1 T C 7: 28,884,465 (GRCm39) D958G probably damaging Het
Ccar2 T G 14: 70,377,100 (GRCm39) K787Q probably benign Het
Ccdc191 C T 16: 43,728,998 (GRCm39) T244I probably benign Het
Cd33 A T 7: 43,179,699 (GRCm39) L243Q possibly damaging Het
Cdc37 T C 9: 21,061,143 (GRCm39) Y4C probably damaging Het
Cenpe T G 3: 134,945,541 (GRCm39) N1018K probably benign Het
Crocc G A 4: 140,744,407 (GRCm39) R1830C probably damaging Het
Csmd1 T C 8: 15,967,392 (GRCm39) D3157G probably damaging Het
Dhx57 C T 17: 80,580,477 (GRCm39) V492M probably damaging Het
Dnah2 A T 11: 69,349,011 (GRCm39) I2486N probably benign Het
Dnhd1 C T 7: 105,342,928 (GRCm39) T1424I possibly damaging Het
Dsc3 C T 18: 20,101,411 (GRCm39) A661T probably benign Het
F930015N05Rik A G 11: 64,326,229 (GRCm39) probably benign Het
Fbxo34 C A 14: 47,767,563 (GRCm39) R308S probably damaging Het
Gm10608 CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 9: 118,989,784 (GRCm39) probably benign Het
Gm11595 A T 11: 99,663,327 (GRCm39) C118S unknown Het
Gm9742 A T 13: 8,085,011 (GRCm39) noncoding transcript Het
Gmeb2 G A 2: 180,900,842 (GRCm39) A185V probably benign Het
Gpr15 A G 16: 58,538,618 (GRCm39) V157A possibly damaging Het
Gpr3 C T 4: 132,937,932 (GRCm39) A247T probably damaging Het
Grin2b A C 6: 135,755,698 (GRCm39) S539A probably benign Het
Hmbs T C 9: 44,252,004 (GRCm39) T92A probably benign Het
Inpp4a A G 1: 37,406,000 (GRCm39) M173V probably benign Het
Irx4 T A 13: 73,413,595 (GRCm39) S22T probably benign Het
Jph3 C T 8: 122,511,881 (GRCm39) A623V probably benign Het
Kif1b G A 4: 149,272,097 (GRCm39) S1568L possibly damaging Het
Ksr1 G A 11: 78,924,139 (GRCm39) S361L probably damaging Het
Lyst T G 13: 13,809,847 (GRCm39) Y506D probably damaging Het
Mctp1 A G 13: 76,972,941 (GRCm39) D648G probably damaging Het
Megf8 T C 7: 25,064,007 (GRCm39) S2788P possibly damaging Het
Mfsd2b T A 12: 4,917,659 (GRCm39) Y129F probably benign Het
Mindy4 T C 6: 55,195,250 (GRCm39) S155P probably benign Het
Mospd4 A G 18: 46,598,731 (GRCm39) noncoding transcript Het
Myo18b A T 5: 112,978,944 (GRCm39) L1223Q probably damaging Het
Nckipsd A G 9: 108,688,932 (GRCm39) T156A probably benign Het
Ndst1 G A 18: 60,824,280 (GRCm39) T799I probably benign Het
Npffr2 A T 5: 89,715,924 (GRCm39) I84F probably damaging Het
Nphp3 G A 9: 103,885,442 (GRCm39) V167M probably damaging Het
Nup107 C A 10: 117,610,380 (GRCm39) R354L possibly damaging Het
Olfml2a T C 2: 38,831,699 (GRCm39) C93R probably damaging Het
Or12e10 A G 2: 87,640,685 (GRCm39) I174V probably benign Het
Or1e25 C G 11: 73,493,631 (GRCm39) S75C possibly damaging Het
Or5l14 A T 2: 87,793,176 (GRCm39) V20D probably benign Het
Pappa T A 4: 65,215,494 (GRCm39) L1134M probably damaging Het
Plscr4 T G 9: 92,370,683 (GRCm39) F217V possibly damaging Het
Pnpla8 T A 12: 44,354,840 (GRCm39) Y667N probably benign Het
Polg A G 7: 79,114,676 (GRCm39) L95P probably damaging Het
Psg20 T G 7: 18,416,643 (GRCm39) I158L probably damaging Het
Pwwp2a A G 11: 43,596,145 (GRCm39) S437G probably benign Het
Rdx A G 9: 51,981,032 (GRCm39) M305V possibly damaging Het
Rinl A G 7: 28,496,168 (GRCm39) E383G probably damaging Het
Ror1 A G 4: 100,299,290 (GRCm39) M888V probably benign Het
Rps12 A T 10: 23,662,776 (GRCm39) I22K possibly damaging Het
Ryr2 G A 13: 11,727,081 (GRCm39) P2427S probably damaging Het
Slc10a6 A G 5: 103,756,922 (GRCm39) Y281H probably benign Het
Slc39a11 A G 11: 113,260,629 (GRCm39) S176P probably benign Het
Slfn10-ps A G 11: 82,921,168 (GRCm39) noncoding transcript Het
Spef2 T C 15: 9,729,747 (GRCm39) T124A possibly damaging Het
Sult2a4 G T 7: 13,649,185 (GRCm39) P207Q probably damaging Het
Tas1r3 G A 4: 155,944,927 (GRCm39) R765C probably damaging Het
Tcstv1a T C 13: 120,355,282 (GRCm39) T117A probably damaging Het
Tha1 A G 11: 117,760,600 (GRCm39) V208A probably damaging Het
Tmbim4 T A 10: 120,060,658 (GRCm39) I215N probably damaging Het
Tmem202 T A 9: 59,427,483 (GRCm39) I122F probably benign Het
Tomm70a T C 16: 56,942,234 (GRCm39) S4P unknown Het
Tpcn2 A G 7: 144,827,712 (GRCm39) probably benign Het
Trim36 A T 18: 46,345,404 (GRCm39) F10I probably benign Het
Usp30 A G 5: 114,249,224 (GRCm39) E176G probably damaging Het
Usp8 T G 2: 126,579,495 (GRCm39) probably null Het
Vmn1r32 T A 6: 66,530,533 (GRCm39) Y81F probably benign Het
Vps36 G T 8: 22,708,305 (GRCm39) probably null Het
Wdr87-ps T C 7: 29,236,565 (GRCm39) noncoding transcript Het
Wnt3 A G 11: 103,703,474 (GRCm39) H319R possibly damaging Het
Zfp319 A T 8: 96,050,391 (GRCm39) probably benign Het
Zfp408 T C 2: 91,475,519 (GRCm39) E545G probably damaging Het
Zfp799 C T 17: 33,038,472 (GRCm39) R598Q possibly damaging Het
Zfp831 T C 2: 174,489,917 (GRCm39) V1228A probably benign Het
Zfp938 T C 10: 82,061,876 (GRCm39) D248G probably benign Het
Other mutations in Rtca
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00228:Rtca APN 3 116,298,110 (GRCm39) missense probably damaging 0.96
IGL02793:Rtca APN 3 116,286,726 (GRCm39) missense probably damaging 1.00
IGL03028:Rtca APN 3 116,286,741 (GRCm39) unclassified probably benign
R1749:Rtca UTSW 3 116,291,293 (GRCm39) missense possibly damaging 0.83
R1858:Rtca UTSW 3 116,287,764 (GRCm39) missense probably benign 0.30
R3083:Rtca UTSW 3 116,301,674 (GRCm39) start gained probably benign
R3750:Rtca UTSW 3 116,286,650 (GRCm39) missense probably benign 0.02
R5493:Rtca UTSW 3 116,293,280 (GRCm39) missense probably benign
R5502:Rtca UTSW 3 116,282,931 (GRCm39) nonsense probably null
R5889:Rtca UTSW 3 116,293,232 (GRCm39) missense possibly damaging 0.87
R6151:Rtca UTSW 3 116,301,476 (GRCm39) missense probably benign 0.04
R6763:Rtca UTSW 3 116,301,398 (GRCm39) critical splice donor site probably null
R8184:Rtca UTSW 3 116,301,473 (GRCm39) missense probably benign 0.01
R8710:Rtca UTSW 3 116,291,303 (GRCm39) missense probably benign 0.02
R9180:Rtca UTSW 3 116,282,905 (GRCm39) missense probably benign 0.17
R9502:Rtca UTSW 3 116,301,413 (GRCm39) missense probably benign 0.03
R9685:Rtca UTSW 3 116,293,225 (GRCm39) missense probably benign 0.19
Z1176:Rtca UTSW 3 116,282,952 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- AGTGATTCACTGAACTGCTGTTTGAG -3'
(R):5'- GAAGTTAGTGCTCTTTCTAGAAGTG -3'

Sequencing Primer
(F):5'- GGAATGGCCTTACACATACACTG -3'
(R):5'- TCTAGAAGTGTAAAAATGATACGTGG -3'
Posted On 2014-09-17