Incidental Mutation 'R5454:Synpo2l'
ID 432689
Institutional Source Beutler Lab
Gene Symbol Synpo2l
Ensembl Gene ENSMUSG00000039376
Gene Name synaptopodin 2-like
Synonyms 1110054M18Rik, Chap
MMRRC Submission 043018-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.814) question?
Stock # R5454 (G1)
Quality Score 225
Status Validated
Chromosome 14
Chromosomal Location 20709014-20718422 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 20712360 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Serine at position 87 (A87S)
Ref Sequence ENSEMBL: ENSMUSP00000112760 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000057090] [ENSMUST00000117386] [ENSMUST00000119483]
AlphaFold Q8BWB1
Predicted Effect probably damaging
Transcript: ENSMUST00000057090
AA Change: A313S

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000053176
Gene: ENSMUSG00000039376
AA Change: A313S

DomainStartEndE-ValueType
PDZ 15 85 3.52e-10 SMART
low complexity region 101 112 N/A INTRINSIC
low complexity region 151 162 N/A INTRINSIC
low complexity region 202 230 N/A INTRINSIC
low complexity region 243 257 N/A INTRINSIC
low complexity region 429 444 N/A INTRINSIC
low complexity region 500 518 N/A INTRINSIC
low complexity region 530 540 N/A INTRINSIC
low complexity region 563 580 N/A INTRINSIC
low complexity region 591 604 N/A INTRINSIC
low complexity region 700 726 N/A INTRINSIC
low complexity region 781 797 N/A INTRINSIC
low complexity region 867 880 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000117386
AA Change: A316S

PolyPhen 2 Score 0.923 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000112792
Gene: ENSMUSG00000039376
AA Change: A316S

DomainStartEndE-ValueType
PDZ 15 88 1.34e-15 SMART
low complexity region 104 115 N/A INTRINSIC
low complexity region 154 165 N/A INTRINSIC
low complexity region 205 233 N/A INTRINSIC
low complexity region 246 260 N/A INTRINSIC
low complexity region 432 447 N/A INTRINSIC
low complexity region 503 521 N/A INTRINSIC
low complexity region 533 543 N/A INTRINSIC
low complexity region 566 583 N/A INTRINSIC
low complexity region 594 607 N/A INTRINSIC
low complexity region 703 729 N/A INTRINSIC
low complexity region 784 800 N/A INTRINSIC
low complexity region 870 883 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000119483
AA Change: A87S

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000112760
Gene: ENSMUSG00000039376
AA Change: A87S

DomainStartEndE-ValueType
low complexity region 203 218 N/A INTRINSIC
low complexity region 274 292 N/A INTRINSIC
low complexity region 304 314 N/A INTRINSIC
low complexity region 337 354 N/A INTRINSIC
low complexity region 365 378 N/A INTRINSIC
low complexity region 474 500 N/A INTRINSIC
low complexity region 555 571 N/A INTRINSIC
low complexity region 641 654 N/A INTRINSIC
Meta Mutation Damage Score 0.0992 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.2%
  • 20x: 95.1%
Validation Efficiency 100% (60/60)
Allele List at MGI
Other mutations in this stock
Total: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930579C12Rik T C 9: 89,051,041 (GRCm39) noncoding transcript Het
Ankfy1 A T 11: 72,637,757 (GRCm39) H483L probably benign Het
Ankrd46 C T 15: 36,479,447 (GRCm39) G215R probably damaging Het
Apobec1 T C 6: 122,558,327 (GRCm39) I143V probably benign Het
Atp2b4 C A 1: 133,657,610 (GRCm39) V627F probably damaging Het
Ccdc80 T A 16: 44,947,588 (GRCm39) Y855* probably null Het
Cd209b T C 8: 3,975,396 (GRCm39) E88G probably damaging Het
Ceacam14 T G 7: 17,548,110 (GRCm39) W67G probably damaging Het
Cope T C 8: 70,757,306 (GRCm39) V50A probably benign Het
Dcaf13 C A 15: 38,987,759 (GRCm39) D168E probably benign Het
Dhcr7 T G 7: 143,391,576 (GRCm39) M55R probably damaging Het
Enpp7 A T 11: 118,879,634 (GRCm39) Y96F probably benign Het
Esco1 T C 18: 10,584,327 (GRCm39) D60G probably benign Het
Fgfr3 G A 5: 33,880,642 (GRCm39) probably benign Het
Frzb T C 2: 80,248,259 (GRCm39) D280G probably damaging Het
Gcat A G 15: 78,920,610 (GRCm39) I317V probably benign Het
Gm13030 A T 4: 138,600,820 (GRCm39) probably benign Het
Gmds A G 13: 32,312,024 (GRCm39) L135P probably damaging Het
Htra2 G A 6: 83,030,995 (GRCm39) P138L probably damaging Het
Il5 A G 11: 53,614,626 (GRCm39) N89S probably damaging Het
Ints3 G A 3: 90,315,834 (GRCm39) T310M possibly damaging Het
Itih2 T C 2: 10,102,804 (GRCm39) I777V probably null Het
Kctd9 T C 14: 67,977,836 (GRCm39) L382S probably damaging Het
Loricrin A G 3: 91,988,789 (GRCm39) S166P unknown Het
Mga T A 2: 119,733,810 (GRCm39) N219K probably damaging Het
Mtmr4 A T 11: 87,501,868 (GRCm39) R641* probably null Het
Muc6 C T 7: 141,235,078 (GRCm39) A611T possibly damaging Het
Obox3-ps8 A T 17: 36,763,903 (GRCm39) noncoding transcript Het
Or5p54 A T 7: 107,554,096 (GRCm39) M83L probably benign Het
Otud4 C T 8: 80,377,671 (GRCm39) L111F possibly damaging Het
Pcdhga12 T A 18: 37,899,314 (GRCm39) S49T possibly damaging Het
Pcdhgc3 A G 18: 37,941,549 (GRCm39) D650G probably damaging Het
Pcmt1 A G 10: 7,516,509 (GRCm39) V167A probably damaging Het
Pcnt A T 10: 76,225,381 (GRCm39) probably null Het
Pcx G T 19: 4,652,504 (GRCm39) V164F probably damaging Het
Plekhg4 T C 8: 106,102,745 (GRCm39) probably null Het
Pmch A G 10: 87,927,707 (GRCm39) E136G probably damaging Het
Prkar1a A G 11: 109,550,886 (GRCm39) D80G probably benign Het
Ryr3 T C 2: 112,560,647 (GRCm39) probably null Het
Slc10a7 T C 8: 79,413,253 (GRCm39) S171P possibly damaging Het
Sox6 A T 7: 115,301,008 (GRCm39) M153K possibly damaging Het
Srgap2 T C 1: 131,217,475 (GRCm39) I946V probably benign Het
Strbp T C 2: 37,535,495 (GRCm39) E71G probably benign Het
Tnrc18 T C 5: 142,757,446 (GRCm39) D1025G unknown Het
Tnxb A G 17: 34,928,599 (GRCm39) H2671R possibly damaging Het
Tor1b GGACG GG 2: 30,846,957 (GRCm39) probably benign Het
Umodl1 A T 17: 31,205,439 (GRCm39) D649V possibly damaging Het
Usp13 G T 3: 32,959,585 (GRCm39) A559S probably damaging Het
Vps45 G A 3: 95,926,969 (GRCm39) P526L probably benign Het
Zfp687 A G 3: 94,916,457 (GRCm39) V855A probably damaging Het
Zfp771 T A 7: 126,853,448 (GRCm39) C205S probably damaging Het
Other mutations in Synpo2l
AlleleSourceChrCoordTypePredicted EffectPPH Score
R0048:Synpo2l UTSW 14 20,716,340 (GRCm39) unclassified probably benign
R0277:Synpo2l UTSW 14 20,711,856 (GRCm39) missense probably damaging 1.00
R0440:Synpo2l UTSW 14 20,711,466 (GRCm39) missense possibly damaging 0.89
R0540:Synpo2l UTSW 14 20,710,748 (GRCm39) missense probably damaging 1.00
R0607:Synpo2l UTSW 14 20,710,748 (GRCm39) missense probably damaging 1.00
R0712:Synpo2l UTSW 14 20,711,907 (GRCm39) missense probably damaging 1.00
R1175:Synpo2l UTSW 14 20,718,235 (GRCm39) missense possibly damaging 0.93
R1563:Synpo2l UTSW 14 20,711,346 (GRCm39) missense probably damaging 1.00
R1729:Synpo2l UTSW 14 20,715,887 (GRCm39) missense probably damaging 1.00
R1730:Synpo2l UTSW 14 20,715,887 (GRCm39) missense probably damaging 1.00
R1739:Synpo2l UTSW 14 20,715,887 (GRCm39) missense probably damaging 1.00
R2199:Synpo2l UTSW 14 20,711,987 (GRCm39) missense probably benign 0.00
R2213:Synpo2l UTSW 14 20,710,734 (GRCm39) missense probably damaging 1.00
R3085:Synpo2l UTSW 14 20,712,248 (GRCm39) missense probably damaging 1.00
R4787:Synpo2l UTSW 14 20,711,765 (GRCm39) missense possibly damaging 0.49
R5256:Synpo2l UTSW 14 20,711,082 (GRCm39) missense probably benign 0.00
R5455:Synpo2l UTSW 14 20,712,360 (GRCm39) missense probably damaging 0.99
R5765:Synpo2l UTSW 14 20,716,198 (GRCm39) missense possibly damaging 0.95
R5950:Synpo2l UTSW 14 20,716,003 (GRCm39) missense probably benign 0.00
R6376:Synpo2l UTSW 14 20,710,702 (GRCm39) missense probably damaging 1.00
R6438:Synpo2l UTSW 14 20,711,204 (GRCm39) missense probably benign 0.00
R6440:Synpo2l UTSW 14 20,718,244 (GRCm39) missense probably damaging 0.98
R6511:Synpo2l UTSW 14 20,712,518 (GRCm39) missense probably damaging 1.00
R6834:Synpo2l UTSW 14 20,710,702 (GRCm39) missense probably damaging 1.00
R7735:Synpo2l UTSW 14 20,711,243 (GRCm39) missense possibly damaging 0.88
R7968:Synpo2l UTSW 14 20,716,870 (GRCm39) splice site probably null
R8250:Synpo2l UTSW 14 20,712,344 (GRCm39) missense probably benign 0.03
R8282:Synpo2l UTSW 14 20,711,204 (GRCm39) missense probably benign 0.00
R8359:Synpo2l UTSW 14 20,716,208 (GRCm39) missense probably benign
R8771:Synpo2l UTSW 14 20,710,491 (GRCm39) missense probably damaging 0.98
R8853:Synpo2l UTSW 14 20,711,442 (GRCm39) missense probably damaging 1.00
R9136:Synpo2l UTSW 14 20,715,857 (GRCm39) missense probably damaging 0.97
R9253:Synpo2l UTSW 14 20,716,738 (GRCm39) missense possibly damaging 0.52
R9705:Synpo2l UTSW 14 20,710,989 (GRCm39) missense probably damaging 0.99
Z1088:Synpo2l UTSW 14 20,716,035 (GRCm39) missense probably damaging 0.99
Z1177:Synpo2l UTSW 14 20,710,572 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- ACTCTCTGCTGTGCCTAAGC -3'
(R):5'- CAGGATTAGAACAGGCCGTG -3'

Sequencing Primer
(F):5'- TGTGCCTAAGCCAGCCCTAG -3'
(R):5'- GTGAAGCCCCCTGATTGATC -3'
Posted On 2016-10-06