Incidental Mutation 'R4879:Snapc4'
ID 375105
Institutional Source Beutler Lab
Gene Symbol Snapc4
Ensembl Gene ENSMUSG00000036281
Gene Name small nuclear RNA activating complex, polypeptide 4
Synonyms 5730436L13Rik
MMRRC Submission 042488-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4879 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 26252777-26270665 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 26256004 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Asparagine at position 840 (S840N)
Ref Sequence ENSEMBL: ENSMUSP00000109750 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000035427] [ENSMUST00000114115]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000035427
AA Change: S832N

PolyPhen 2 Score 0.928 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000041767
Gene: ENSMUSG00000036281
AA Change: S832N

DomainStartEndE-ValueType
low complexity region 33 52 N/A INTRINSIC
low complexity region 60 72 N/A INTRINSIC
coiled coil region 93 119 N/A INTRINSIC
low complexity region 200 212 N/A INTRINSIC
SANT 219 290 2.37e1 SMART
SANT 293 343 4.38e-10 SMART
SANT 345 397 3.05e-9 SMART
SANT 400 449 8.24e-15 SMART
SANT 452 501 7.8e-16 SMART
low complexity region 516 547 N/A INTRINSIC
Blast:SANT 550 753 1e-23 BLAST
low complexity region 893 909 N/A INTRINSIC
low complexity region 925 947 N/A INTRINSIC
low complexity region 971 983 N/A INTRINSIC
low complexity region 988 1007 N/A INTRINSIC
low complexity region 1157 1169 N/A INTRINSIC
low complexity region 1176 1190 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000114115
AA Change: S840N

PolyPhen 2 Score 0.928 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000109750
Gene: ENSMUSG00000036281
AA Change: S840N

DomainStartEndE-ValueType
coiled coil region 3 29 N/A INTRINSIC
low complexity region 41 60 N/A INTRINSIC
low complexity region 68 80 N/A INTRINSIC
coiled coil region 101 127 N/A INTRINSIC
low complexity region 208 220 N/A INTRINSIC
SANT 227 298 2.37e1 SMART
SANT 301 351 4.38e-10 SMART
SANT 353 405 3.05e-9 SMART
SANT 408 457 8.24e-15 SMART
SANT 460 509 7.8e-16 SMART
low complexity region 524 555 N/A INTRINSIC
Blast:SANT 558 761 1e-23 BLAST
low complexity region 901 917 N/A INTRINSIC
low complexity region 933 955 N/A INTRINSIC
low complexity region 979 991 N/A INTRINSIC
low complexity region 996 1015 N/A INTRINSIC
low complexity region 1165 1177 N/A INTRINSIC
low complexity region 1184 1198 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000123934
SMART Domains Protein: ENSMUSP00000122456
Gene: ENSMUSG00000036281

DomainStartEndE-ValueType
SANT 47 99 3.05e-9 SMART
SANT 102 151 8.24e-15 SMART
SANT 154 203 7.8e-16 SMART
low complexity region 218 249 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125198
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125789
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133778
Predicted Effect noncoding transcript
Transcript: ENSMUST00000149850
Predicted Effect noncoding transcript
Transcript: ENSMUST00000150121
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135171
Predicted Effect noncoding transcript
Transcript: ENSMUST00000149316
Predicted Effect noncoding transcript
Transcript: ENSMUST00000136054
Predicted Effect noncoding transcript
Transcript: ENSMUST00000148024
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137869
Meta Mutation Damage Score 0.1240 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.4%
Validation Efficiency 97% (86/89)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the largest subunit of the small nuclear RNA-activating protein (SNAP) complex. The encoded protein contains a Myb DNA-binding domain, and is essential for RNA polymerase II and III polymerase transcription from small nuclear RNA promoters. A mutation in this gene is associated with ankylosing spondylitis. [provided by RefSeq, Jul 2016]
Allele List at MGI
Other mutations in this stock
Total: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca6 T A 11: 110,110,526 (GRCm39) Y541F probably damaging Het
Acot12 T A 13: 91,911,083 (GRCm39) V136E probably benign Het
Aftph A G 11: 20,648,311 (GRCm39) probably null Het
Ambra1 C T 2: 91,603,039 (GRCm39) probably benign Het
Anks6 C T 4: 47,030,795 (GRCm39) G601S probably damaging Het
Ano9 T C 7: 140,690,415 (GRCm39) D73G probably benign Het
Asap3 G A 4: 135,969,975 (GRCm39) D778N probably benign Het
Atp8a2 G T 14: 60,245,918 (GRCm39) Y591* probably null Het
Blk T C 14: 63,613,414 (GRCm39) T365A probably benign Het
C4b G T 17: 34,962,621 (GRCm39) S27Y probably damaging Het
C6 G T 15: 4,833,129 (GRCm39) probably null Het
Ccdc33 T A 9: 57,974,839 (GRCm39) I345F possibly damaging Het
Cetn3 T A 13: 81,940,268 (GRCm39) probably benign Het
Cntn3 T A 6: 102,244,389 (GRCm39) I387L possibly damaging Het
Cog8 A G 8: 107,782,984 (GRCm39) C102R probably damaging Het
Cspg4b T C 13: 113,456,321 (GRCm39) I789T probably benign Het
Cyp2c55 CA C 19: 39,030,522 (GRCm39) probably null Het
Defa40 T A 8: 21,740,380 (GRCm39) L62Q probably damaging Het
Dmxl1 C T 18: 50,022,534 (GRCm39) A1624V probably damaging Het
Dnah1 T G 14: 31,022,705 (GRCm39) E1144A possibly damaging Het
Dnah12 T A 14: 26,439,201 (GRCm39) probably null Het
Dnah2 G A 11: 69,367,517 (GRCm39) T1794I probably damaging Het
Entrep1 T C 19: 23,953,019 (GRCm39) probably null Het
Erbin A T 13: 103,971,282 (GRCm39) M778K probably benign Het
Fbxw10 G T 11: 62,738,573 (GRCm39) A156S probably damaging Het
Flnc T A 6: 29,460,805 (GRCm39) F2632Y probably damaging Het
Frmd4a A G 2: 4,534,628 (GRCm39) K160E probably damaging Het
Glipr1l2 A G 10: 111,943,029 (GRCm39) K295E probably benign Het
Herc1 T A 9: 66,370,119 (GRCm39) C465* probably null Het
Hoxb4 A G 11: 96,211,014 (GRCm39) I205V probably damaging Het
Ikbke GCC G 1: 131,203,004 (GRCm39) probably null Het
Il36a A G 2: 24,106,032 (GRCm39) N29S probably benign Het
Ilk A G 7: 105,391,011 (GRCm39) S292G probably benign Het
Itgb5 G C 16: 33,696,348 (GRCm39) G180R probably damaging Het
Josd1-ps T C 7: 27,648,768 (GRCm39) noncoding transcript Het
Kcnip4 T C 5: 48,567,207 (GRCm39) D120G possibly damaging Het
Kin A G 2: 10,085,455 (GRCm39) D5G probably benign Het
Lrrtm2 C A 18: 35,346,372 (GRCm39) G310V probably damaging Het
Med1 T C 11: 98,046,186 (GRCm39) probably benign Het
Mepce C A 5: 137,783,544 (GRCm39) probably benign Het
Nckipsd T A 9: 108,691,114 (GRCm39) probably benign Het
Notch3 T A 17: 32,366,937 (GRCm39) Q866L probably benign Het
Or52b4 A T 7: 102,183,962 (GRCm39) T3S probably benign Het
Or5l14 A T 2: 87,793,040 (GRCm39) H65Q possibly damaging Het
Or8k20 A T 2: 86,106,107 (GRCm39) C241* probably null Het
Orai1 T C 5: 123,149,894 (GRCm39) probably benign Het
Pate12 G A 9: 36,344,089 (GRCm39) C24Y probably damaging Het
Pcdhb8 A T 18: 37,489,219 (GRCm39) E299V probably damaging Het
Pcnx4 G A 12: 72,613,959 (GRCm39) D635N probably damaging Het
Pex5 T C 6: 124,375,322 (GRCm39) I567V probably benign Het
Ppfibp2 T C 7: 107,328,390 (GRCm39) S485P probably benign Het
Sbno1 T C 5: 124,542,087 (GRCm39) Y356C probably damaging Het
Sdcbp T C 4: 6,381,056 (GRCm39) I67T possibly damaging Het
Slc5a7 A G 17: 54,583,679 (GRCm39) I537T probably benign Het
Slc66a1 A T 4: 139,029,095 (GRCm39) probably null Het
Smad4 A G 18: 73,774,974 (GRCm39) C442R probably damaging Het
Smpd5 A G 15: 76,179,070 (GRCm39) H146R possibly damaging Het
Snai2 A G 16: 14,524,605 (GRCm39) Y37C probably benign Het
Stpg2 T C 3: 138,921,134 (GRCm39) I113T probably benign Het
Tbc1d32 T C 10: 55,925,125 (GRCm39) probably null Het
Tfg A T 16: 56,521,520 (GRCm39) S39R probably damaging Het
Thsd7b T A 1: 130,116,236 (GRCm39) S1330T possibly damaging Het
Tnfaip3 T C 10: 18,881,321 (GRCm39) T322A probably benign Het
Tpra1 A G 6: 88,888,691 (GRCm39) Y291C probably damaging Het
Trcg1 A G 9: 57,154,003 (GRCm39) D658G probably damaging Het
Trip4 C T 9: 65,782,304 (GRCm39) V143I probably benign Het
Trp53bp1 T C 2: 121,033,084 (GRCm39) K1691E probably damaging Het
Ttc8 T A 12: 98,908,562 (GRCm39) M77K possibly damaging Het
Tubb2a A T 13: 34,258,572 (GRCm39) M406K probably benign Het
Txnrd1 T A 10: 82,717,751 (GRCm39) probably null Het
Ugt2a3 C A 5: 87,479,144 (GRCm39) R268L probably benign Het
Usp34 T G 11: 23,323,410 (GRCm39) M982R possibly damaging Het
Vmn2r43 T A 7: 8,258,102 (GRCm39) K370N probably benign Het
Vopp1 A T 6: 57,739,355 (GRCm39) probably benign Het
Vps11 A C 9: 44,264,597 (GRCm39) C660G probably benign Het
Wnk1 T C 6: 119,926,338 (GRCm39) H1137R probably damaging Het
Wtap A G 17: 13,188,322 (GRCm39) Y193H probably damaging Het
Zfp462 T A 4: 55,009,444 (GRCm39) V470D probably benign Het
Other mutations in Snapc4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00162:Snapc4 APN 2 26,259,324 (GRCm39) missense probably benign
IGL01730:Snapc4 APN 2 26,253,736 (GRCm39) splice site probably null
IGL01958:Snapc4 APN 2 26,256,452 (GRCm39) unclassified probably benign
IGL02354:Snapc4 APN 2 26,257,319 (GRCm39) unclassified probably benign
IGL02425:Snapc4 APN 2 26,258,212 (GRCm39) missense probably damaging 1.00
IGL02812:Snapc4 APN 2 26,259,384 (GRCm39) missense probably benign 0.03
IGL02951:Snapc4 APN 2 26,260,847 (GRCm39) missense probably benign 0.33
R0011:Snapc4 UTSW 2 26,254,825 (GRCm39) missense probably benign 0.03
R0409:Snapc4 UTSW 2 26,257,228 (GRCm39) missense probably benign 0.37
R0932:Snapc4 UTSW 2 26,264,658 (GRCm39) missense probably damaging 1.00
R1674:Snapc4 UTSW 2 26,266,209 (GRCm39) missense probably benign
R1878:Snapc4 UTSW 2 26,266,165 (GRCm39) critical splice donor site probably null
R3722:Snapc4 UTSW 2 26,255,440 (GRCm39) missense probably benign
R3886:Snapc4 UTSW 2 26,255,510 (GRCm39) nonsense probably null
R3887:Snapc4 UTSW 2 26,255,510 (GRCm39) nonsense probably null
R3888:Snapc4 UTSW 2 26,255,510 (GRCm39) nonsense probably null
R3889:Snapc4 UTSW 2 26,255,510 (GRCm39) nonsense probably null
R4638:Snapc4 UTSW 2 26,255,314 (GRCm39) missense probably damaging 1.00
R4663:Snapc4 UTSW 2 26,264,193 (GRCm39) missense possibly damaging 0.77
R4922:Snapc4 UTSW 2 26,259,245 (GRCm39) missense probably benign
R5385:Snapc4 UTSW 2 26,264,515 (GRCm39) missense probably benign 0.44
R5525:Snapc4 UTSW 2 26,259,538 (GRCm39) small deletion probably benign
R5762:Snapc4 UTSW 2 26,268,618 (GRCm39) missense probably damaging 1.00
R5839:Snapc4 UTSW 2 26,255,546 (GRCm39) missense probably benign 0.01
R6300:Snapc4 UTSW 2 26,268,563 (GRCm39) missense probably benign 0.14
R6422:Snapc4 UTSW 2 26,258,315 (GRCm39) missense probably benign 0.00
R6843:Snapc4 UTSW 2 26,263,611 (GRCm39) missense probably benign 0.03
R7044:Snapc4 UTSW 2 26,259,965 (GRCm39) missense probably damaging 1.00
R7341:Snapc4 UTSW 2 26,259,273 (GRCm39) missense probably benign 0.01
R7727:Snapc4 UTSW 2 26,263,446 (GRCm39) missense probably damaging 1.00
R7941:Snapc4 UTSW 2 26,266,730 (GRCm39) missense probably damaging 0.98
R8277:Snapc4 UTSW 2 26,255,722 (GRCm39) missense probably benign 0.05
R8311:Snapc4 UTSW 2 26,268,546 (GRCm39) missense probably benign
R8323:Snapc4 UTSW 2 26,254,711 (GRCm39) missense probably benign 0.15
R8777:Snapc4 UTSW 2 26,259,375 (GRCm39) missense probably benign 0.00
R8777-TAIL:Snapc4 UTSW 2 26,259,375 (GRCm39) missense probably benign 0.00
R8855:Snapc4 UTSW 2 26,264,545 (GRCm39) missense probably damaging 1.00
R9069:Snapc4 UTSW 2 26,260,805 (GRCm39) nonsense probably null
R9362:Snapc4 UTSW 2 26,254,865 (GRCm39) missense probably damaging 0.99
R9718:Snapc4 UTSW 2 26,268,533 (GRCm39) missense probably damaging 1.00
R9780:Snapc4 UTSW 2 26,267,019 (GRCm39) missense possibly damaging 0.94
X0010:Snapc4 UTSW 2 26,259,973 (GRCm39) missense probably damaging 1.00
X0011:Snapc4 UTSW 2 26,259,973 (GRCm39) missense probably damaging 1.00
X0014:Snapc4 UTSW 2 26,259,973 (GRCm39) missense probably damaging 1.00
X0017:Snapc4 UTSW 2 26,259,973 (GRCm39) missense probably damaging 1.00
X0021:Snapc4 UTSW 2 26,259,973 (GRCm39) missense probably damaging 1.00
X0023:Snapc4 UTSW 2 26,259,973 (GRCm39) missense probably damaging 1.00
X0028:Snapc4 UTSW 2 26,259,973 (GRCm39) missense probably damaging 1.00
X0033:Snapc4 UTSW 2 26,259,973 (GRCm39) missense probably damaging 1.00
X0064:Snapc4 UTSW 2 26,259,973 (GRCm39) missense probably damaging 1.00
X0067:Snapc4 UTSW 2 26,259,973 (GRCm39) missense probably damaging 1.00
Z1176:Snapc4 UTSW 2 26,258,234 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AGCTGGCTGTTGAGACCAAG -3'
(R):5'- AGCCAGTCTTTCATAGTCGG -3'

Sequencing Primer
(F):5'- CTGTTGAGACCAAGAGCCTG -3'
(R):5'- CAGTCTTTCATAGTCGGGCTGC -3'
Posted On 2016-03-17