Incidental Mutation 'R2100:Ythdc1'
ID 230424
Institutional Source Beutler Lab
Gene Symbol Ythdc1
Ensembl Gene ENSMUSG00000035851
Gene Name YTH domain containing 1
Synonyms A730098D12Rik
MMRRC Submission 040104-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.968) question?
Stock # R2100 (G1)
Quality Score 225
Status Not validated
Chromosome 5
Chromosomal Location 86952080-86984518 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 86964544 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 130 (S130T)
Ref Sequence ENSEMBL: ENSMUSP00000122491 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000038384] [ENSMUST00000119339] [ENSMUST00000120498] [ENSMUST00000156363]
AlphaFold E9Q5K9
Predicted Effect probably benign
Transcript: ENSMUST00000038384
AA Change: S118T

PolyPhen 2 Score 0.177 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000039133
Gene: ENSMUSG00000035851
AA Change: S118T

DomainStartEndE-ValueType
SCOP:d1qbkb_ 225 249 6e-3 SMART
low complexity region 269 280 N/A INTRINSIC
low complexity region 316 330 N/A INTRINSIC
Pfam:YTH 356 494 5e-42 PFAM
low complexity region 516 540 N/A INTRINSIC
low complexity region 609 622 N/A INTRINSIC
low complexity region 625 645 N/A INTRINSIC
low complexity region 682 736 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000119339
AA Change: S118T

PolyPhen 2 Score 0.177 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000113000
Gene: ENSMUSG00000035851
AA Change: S118T

DomainStartEndE-ValueType
SCOP:d1qbkb_ 225 249 6e-3 SMART
low complexity region 269 280 N/A INTRINSIC
Pfam:YTH 337 478 4.4e-44 PFAM
low complexity region 498 522 N/A INTRINSIC
low complexity region 583 596 N/A INTRINSIC
low complexity region 599 619 N/A INTRINSIC
low complexity region 656 710 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000120498
AA Change: S118T

PolyPhen 2 Score 0.177 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000113951
Gene: ENSMUSG00000035851
AA Change: S118T

DomainStartEndE-ValueType
SCOP:d1qbkb_ 225 249 6e-3 SMART
low complexity region 269 280 N/A INTRINSIC
low complexity region 316 330 N/A INTRINSIC
Pfam:YTH 355 496 4.6e-44 PFAM
low complexity region 516 540 N/A INTRINSIC
low complexity region 601 614 N/A INTRINSIC
low complexity region 617 637 N/A INTRINSIC
low complexity region 674 728 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000151489
Predicted Effect possibly damaging
Transcript: ENSMUST00000156363
AA Change: S130T

PolyPhen 2 Score 0.619 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000122491
Gene: ENSMUSG00000035851
AA Change: S130T

DomainStartEndE-ValueType
SCOP:d1qbkb_ 237 261 8e-3 SMART
low complexity region 281 292 N/A INTRINSIC
Pfam:YTH 350 488 3e-42 PFAM
low complexity region 510 525 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000198859
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.4%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca3 C T 17: 24,627,183 (GRCm39) R1295W probably damaging Het
Abca8b A T 11: 109,828,608 (GRCm39) I1430N probably damaging Het
Abcb1a A G 5: 8,763,202 (GRCm39) T577A probably damaging Het
Arl5b G A 2: 15,078,006 (GRCm39) M101I probably benign Het
C1qbp T A 11: 70,868,928 (GRCm39) N278I probably benign Het
Cdh1 A T 8: 107,386,300 (GRCm39) T408S possibly damaging Het
Cfap54 T A 10: 92,837,799 (GRCm39) I1034F possibly damaging Het
Chd9 C T 8: 91,760,615 (GRCm39) P2120L probably benign Het
Chil4 T C 3: 106,121,663 (GRCm39) K62R probably benign Het
Crebl2 A G 6: 134,828,166 (GRCm39) T113A probably benign Het
Cyp2c69 C A 19: 39,875,130 (GRCm39) V8L probably benign Het
Dpp6 A G 5: 27,869,742 (GRCm39) R447G probably damaging Het
Efcab6 A T 15: 83,777,168 (GRCm39) probably null Het
Emilin1 T G 5: 31,075,241 (GRCm39) V494G probably benign Het
Enoph1 A G 5: 100,211,645 (GRCm39) I181V probably null Het
F3 T C 3: 121,526,082 (GRCm39) V215A possibly damaging Het
Fads2b T C 2: 85,330,593 (GRCm39) N238S probably damaging Het
Fat3 G T 9: 16,288,726 (GRCm39) H266N possibly damaging Het
Frmd4a A G 2: 4,610,834 (GRCm39) T995A probably damaging Het
Garnl3 T C 2: 32,936,657 (GRCm39) T171A probably benign Het
Hspa4l T C 3: 40,727,090 (GRCm39) V476A possibly damaging Het
Impg2 A G 16: 56,051,748 (GRCm39) probably null Het
Kctd6 T C 14: 8,222,239 (GRCm38) L27P possibly damaging Het
Kmt2d G T 15: 98,744,361 (GRCm39) probably benign Het
Kremen1 AGGCGG AGGCGGCGG 11: 5,151,788 (GRCm39) probably benign Het
Lrig2 A G 3: 104,418,946 (GRCm39) L21P possibly damaging Het
Macf1 G A 4: 123,291,699 (GRCm39) Q3284* probably null Het
Mnt A G 11: 74,722,177 (GRCm39) E8G probably damaging Het
Nbeal1 A G 1: 60,344,430 (GRCm39) probably null Het
Nid2 C T 14: 19,828,946 (GRCm39) Q331* probably null Het
Nlrx1 A G 9: 44,173,905 (GRCm39) L432P probably damaging Het
Nop2 T A 6: 125,117,785 (GRCm39) D445E probably damaging Het
Nup62 T C 7: 44,478,921 (GRCm39) probably benign Het
Oas2 A G 5: 120,883,740 (GRCm39) probably null Het
Or5b121 A G 19: 13,507,798 (GRCm39) I298V probably benign Het
Or5p1 A T 7: 107,916,761 (GRCm39) Y220F probably benign Het
Or5w10 T A 2: 87,375,169 (GRCm39) T240S probably damaging Het
Or8k40 A T 2: 86,584,905 (GRCm39) M59K possibly damaging Het
Or9i14 A G 19: 13,792,600 (GRCm39) M118T possibly damaging Het
P3h3 T A 6: 124,822,005 (GRCm39) T623S probably damaging Het
Pkp3 T C 7: 140,663,205 (GRCm39) V350A probably damaging Het
Plekha3 T A 2: 76,523,007 (GRCm39) I225N probably benign Het
Ptch1 T G 13: 63,672,773 (GRCm39) E944A probably benign Het
Rbp3 C T 14: 33,677,975 (GRCm39) T641M probably damaging Het
Rnf213 A T 11: 119,358,128 (GRCm39) K4292* probably null Het
Rtkn T C 6: 83,126,541 (GRCm39) probably null Het
Secisbp2l C T 2: 125,582,657 (GRCm39) G933D possibly damaging Het
Snx10 T C 6: 51,565,395 (GRCm39) Y171H probably damaging Het
Stx12 A T 4: 132,587,913 (GRCm39) I173N possibly damaging Het
Thrb T A 14: 18,030,393 (GRCm38) M379K possibly damaging Het
Tmem132e T A 11: 82,335,357 (GRCm39) V813E probably damaging Het
Tnfsf12 T C 11: 69,578,175 (GRCm39) E134G probably damaging Het
Tns2 C T 15: 102,017,369 (GRCm39) R281C probably damaging Het
Tpbgl T A 7: 99,275,651 (GRCm39) I69F possibly damaging Het
Zbp1 A G 2: 173,051,037 (GRCm39) S278P probably damaging Het
Zfp30 A G 7: 29,492,951 (GRCm39) T483A probably benign Het
Zfp322a G A 13: 23,541,460 (GRCm39) S94L possibly damaging Het
Zfp646 T G 7: 127,481,359 (GRCm39) Y1179D probably damaging Het
Other mutations in Ythdc1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00676:Ythdc1 APN 5 86,979,670 (GRCm39) missense probably damaging 1.00
IGL02222:Ythdc1 APN 5 86,975,902 (GRCm39) missense possibly damaging 0.72
R0091:Ythdc1 UTSW 5 86,968,560 (GRCm39) intron probably benign
R0311:Ythdc1 UTSW 5 86,983,564 (GRCm39) missense probably damaging 0.97
R0349:Ythdc1 UTSW 5 86,983,579 (GRCm39) missense probably damaging 1.00
R0630:Ythdc1 UTSW 5 86,957,207 (GRCm39) splice site probably benign
R1662:Ythdc1 UTSW 5 86,975,981 (GRCm39) critical splice donor site probably null
R1907:Ythdc1 UTSW 5 86,978,489 (GRCm39) missense probably damaging 1.00
R2911:Ythdc1 UTSW 5 86,964,418 (GRCm39) missense possibly damaging 0.95
R3692:Ythdc1 UTSW 5 86,970,526 (GRCm39) missense probably damaging 0.98
R4042:Ythdc1 UTSW 5 86,964,383 (GRCm39) missense probably benign 0.03
R4398:Ythdc1 UTSW 5 86,983,679 (GRCm39) utr 3 prime probably benign
R4398:Ythdc1 UTSW 5 86,963,513 (GRCm39) missense possibly damaging 0.95
R4608:Ythdc1 UTSW 5 86,970,667 (GRCm39) missense probably damaging 0.97
R4806:Ythdc1 UTSW 5 86,970,704 (GRCm39) missense probably damaging 0.99
R5291:Ythdc1 UTSW 5 86,983,547 (GRCm39) missense probably damaging 1.00
R5761:Ythdc1 UTSW 5 86,983,810 (GRCm39) utr 3 prime probably benign
R6180:Ythdc1 UTSW 5 86,975,953 (GRCm39) missense possibly damaging 0.91
R6249:Ythdc1 UTSW 5 86,979,815 (GRCm39) missense possibly damaging 0.94
R6560:Ythdc1 UTSW 5 86,964,467 (GRCm39) missense probably benign 0.06
R7145:Ythdc1 UTSW 5 86,964,467 (GRCm39) missense probably benign 0.06
R8072:Ythdc1 UTSW 5 86,969,133 (GRCm39) nonsense probably null
R8225:Ythdc1 UTSW 5 86,964,797 (GRCm39) missense possibly damaging 0.73
R8225:Ythdc1 UTSW 5 86,964,796 (GRCm39) missense possibly damaging 0.91
R8229:Ythdc1 UTSW 5 86,957,167 (GRCm39) intron probably benign
R8246:Ythdc1 UTSW 5 86,965,181 (GRCm39) missense possibly damaging 0.94
R8284:Ythdc1 UTSW 5 86,964,325 (GRCm39) missense probably benign 0.18
R8385:Ythdc1 UTSW 5 86,975,961 (GRCm39) missense possibly damaging 0.77
R8546:Ythdc1 UTSW 5 86,974,607 (GRCm39) missense possibly damaging 0.78
Predicted Primers PCR Primer
(F):5'- GAGTCTACTGACACCAAGCG -3'
(R):5'- GCACGTCTATCAACTTCAAGCC -3'

Sequencing Primer
(F):5'- GCGACAAAAACCTTCCATCCATTC -3'
(R):5'- AACTTCAAGCCCAATTCTCTGATG -3'
Posted On 2014-09-18