Incidental Mutation 'R7060:Smarcal1'
ID 548158
Institutional Source Beutler Lab
Gene Symbol Smarcal1
Ensembl Gene ENSMUSG00000039354
Gene Name SWI/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1
Synonyms Mharp, 6030401P21Rik
MMRRC Submission 045157-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R7060 (G1)
Quality Score 221.009
Status Validated
Chromosome 1
Chromosomal Location 72622410-72672293 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 72652101 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 621 (V621A)
Ref Sequence ENSEMBL: ENSMUSP00000137833 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047615] [ENSMUST00000152225]
AlphaFold Q8BJL0
Predicted Effect probably damaging
Transcript: ENSMUST00000047615
AA Change: V621A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000047589
Gene: ENSMUSG00000039354
AA Change: V621A

DomainStartEndE-ValueType
low complexity region 31 51 N/A INTRINSIC
Pfam:HARP 214 268 3.6e-26 PFAM
Pfam:HARP 302 356 1.2e-26 PFAM
DEXDc 391 564 7.01e-17 SMART
low complexity region 632 641 N/A INTRINSIC
HELICc 697 780 8.17e-18 SMART
low complexity region 879 889 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000152225
AA Change: V621A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000137833
Gene: ENSMUSG00000039354
AA Change: V621A

DomainStartEndE-ValueType
low complexity region 31 51 N/A INTRINSIC
Pfam:HARP 214 268 8e-29 PFAM
Pfam:HARP 302 356 3e-26 PFAM
DEXDc 391 564 7.01e-17 SMART
low complexity region 632 641 N/A INTRINSIC
HELICc 697 780 8.17e-18 SMART
low complexity region 879 889 N/A INTRINSIC
Meta Mutation Damage Score 0.7995 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency 96% (78/81)
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 a member of the SWI/SNF family of proteins. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein shows sequence similarity to the E. coli RNA polymerase-binding protein HepA. Mutations in this gene are a cause of Schimke immunoosseous dysplasia (SIOD), an autosomal recessive disorder with the diagnostic features of spondyloepiphyseal dysplasia, renal dysfunction, and T-cell immunodeficiency. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele display reduced B cell counts and increased susceptibility to heat induced mortality. Treatment of homozygous null mice with alpha-amanitin results in phenotypes similar to Schimke Type Immunoosseous Dysplasia. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 79 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcg4 T A 9: 44,186,425 (GRCm39) T535S probably benign Het
Adamts19 A T 18: 58,970,712 (GRCm39) R99* probably null Het
Alg6 C T 4: 99,650,198 (GRCm39) L473F possibly damaging Het
Ankar A T 1: 72,695,272 (GRCm39) N893K probably benign Het
Ankrd54 G A 15: 78,939,739 (GRCm39) A183V possibly damaging Het
Anpep G T 7: 79,491,542 (GRCm39) T153K probably benign Het
Arap1 A G 7: 101,058,564 (GRCm39) probably null Het
Aspg A T 12: 112,089,387 (GRCm39) T392S probably benign Het
B230307C23Rik A C 16: 97,811,331 (GRCm39) R68S probably benign Het
Bdp1 G C 13: 100,196,002 (GRCm39) N1253K probably damaging Het
Ccrl2 G A 9: 110,884,682 (GRCm39) S272F probably damaging Het
Cdon T C 9: 35,398,205 (GRCm39) L974P probably damaging Het
Celsr1 C A 15: 85,916,856 (GRCm39) E372D probably benign Het
Cers1 A T 8: 70,768,555 (GRCm39) M16L possibly damaging Het
Col2a1 G T 15: 97,874,022 (GRCm39) Q1387K unknown Het
Ddx39b G A 17: 35,471,726 (GRCm39) V291M probably damaging Het
Dppa2 T A 16: 48,136,076 (GRCm39) S143T probably benign Het
Dpy19l1 A T 9: 24,334,419 (GRCm39) M583K possibly damaging Het
Eno3 A T 11: 70,552,245 (GRCm39) D299V possibly damaging Het
Epha8 C T 4: 136,658,469 (GRCm39) V969M probably damaging Het
Fcgbp A T 7: 27,791,358 (GRCm39) H873L probably benign Het
Fhad1 CGG CG 4: 141,645,602 (GRCm39) probably null Het
Fntb A C 12: 76,934,649 (GRCm39) N173T possibly damaging Het
Gins2 T A 8: 121,308,880 (GRCm39) M125L probably benign Het
Gys1 G A 7: 45,089,437 (GRCm39) A199T probably damaging Het
Herpud1 C A 8: 95,117,391 (GRCm39) H116N probably benign Het
Hoga1 C A 19: 42,048,685 (GRCm39) Y134* probably null Het
Il10ra A G 9: 45,167,522 (GRCm39) I343T probably benign Het
Inava T C 1: 136,147,935 (GRCm39) K339R possibly damaging Het
Inpp5j C T 11: 3,450,133 (GRCm39) probably null Het
Itpkb T C 1: 180,160,695 (GRCm39) S274P probably damaging Het
Kalrn C T 16: 34,177,418 (GRCm39) C249Y probably damaging Het
Klhl35 G C 7: 99,117,665 (GRCm39) A70P possibly damaging Het
Lhx1 A G 11: 84,411,108 (GRCm39) probably null Het
Lmbrd1 T C 1: 24,732,047 (GRCm39) V88A probably benign Het
Macc1 T G 12: 119,411,190 (GRCm39) L653V probably damaging Het
Madd T C 2: 91,007,452 (GRCm39) D220G probably damaging Het
Mllt10 T A 2: 18,164,371 (GRCm39) H300Q possibly damaging Het
Mlxipl G A 5: 135,161,169 (GRCm39) A363T possibly damaging Het
Mus81 G T 19: 5,537,821 (GRCm39) D78E probably benign Het
Mxd1 A T 6: 86,630,141 (GRCm39) L26M probably damaging Het
Nhsl1 C T 10: 18,402,251 (GRCm39) T1159M probably damaging Het
Nos1ap A G 1: 170,165,694 (GRCm39) S190P possibly damaging Het
Nwd1 A C 8: 73,393,322 (GRCm39) D195A probably damaging Het
Or12d13 G T 17: 37,647,352 (GRCm39) T257N probably benign Het
Or6k4 A T 1: 173,964,376 (GRCm39) D22V probably benign Het
Or8c14-ps1 G A 9: 38,101,392 (GRCm39) V124I probably damaging Het
Or8k24 T A 2: 86,216,569 (GRCm39) R64S possibly damaging Het
Otof T C 5: 30,545,700 (GRCm39) D500G possibly damaging Het
Pcgf5 T A 19: 36,420,339 (GRCm39) Y190* probably null Het
Pdcd11 C T 19: 47,099,418 (GRCm39) T839I probably benign Het
Ppard G C 17: 28,517,886 (GRCm39) S318T probably benign Het
Ppfia2 A G 10: 106,597,970 (GRCm39) K178E probably damaging Het
Ppm1n G T 7: 19,013,187 (GRCm39) R255S probably damaging Het
Ppp1r21 A G 17: 88,887,972 (GRCm39) Y693C probably damaging Het
Ppp2r5d A T 17: 46,998,279 (GRCm39) V169E possibly damaging Het
Prc1 A T 7: 79,954,121 (GRCm39) T53S probably benign Het
Pwp2 A C 10: 78,009,084 (GRCm39) probably null Het
Rab5c G A 11: 100,610,789 (GRCm39) R40C probably damaging Het
Ring1 A G 17: 34,242,364 (GRCm39) C48R probably damaging Het
Rpap1 T C 2: 119,604,043 (GRCm39) D496G probably damaging Het
Rspo4 C A 2: 151,714,998 (GRCm39) Q212K unknown Het
Samd9l T A 6: 3,372,716 (GRCm39) D1515V probably damaging Het
Serinc3 T C 2: 163,478,879 (GRCm39) T83A probably benign Het
Setd5 A C 6: 113,094,343 (GRCm39) D420A probably damaging Het
Sidt2 T C 9: 45,864,544 (GRCm39) T62A possibly damaging Het
Srcin1 A G 11: 97,464,711 (GRCm39) L12P probably damaging Het
Stx18 G A 5: 38,278,599 (GRCm39) D165N possibly damaging Het
Sumf2 A G 5: 129,883,341 (GRCm39) K139E possibly damaging Het
Tdo2 A T 3: 81,876,866 (GRCm39) I102N probably damaging Het
Tdp1 T A 12: 99,877,947 (GRCm39) S410T probably benign Het
Tmem94 A T 11: 115,683,764 (GRCm39) I726F probably damaging Het
Ttc21a A G 9: 119,795,742 (GRCm39) E1192G probably damaging Het
Ttc8 T C 12: 98,909,726 (GRCm39) I52T probably benign Het
Vmn2r99 A T 17: 19,614,826 (GRCm39) R849* probably null Het
Wwc1 T C 11: 35,806,003 (GRCm39) K77E possibly damaging Het
Xirp2 A T 2: 67,345,952 (GRCm39) E2731V probably damaging Het
Zfp1006 A C 8: 129,945,613 (GRCm39) I404R probably benign Het
Zfp423 G A 8: 88,509,507 (GRCm39) T258I probably damaging Het
Other mutations in Smarcal1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01358:Smarcal1 APN 1 72,655,724 (GRCm39) missense possibly damaging 0.80
IGL01658:Smarcal1 APN 1 72,625,290 (GRCm39) missense probably benign 0.00
IGL01980:Smarcal1 APN 1 72,655,679 (GRCm39) nonsense probably null
IGL02007:Smarcal1 APN 1 72,635,099 (GRCm39) missense probably damaging 0.98
IGL02153:Smarcal1 APN 1 72,672,214 (GRCm39) utr 3 prime probably benign
IGL02496:Smarcal1 APN 1 72,659,247 (GRCm39) missense probably damaging 1.00
IGL03084:Smarcal1 APN 1 72,638,094 (GRCm39) splice site probably null
IGL03135:Smarcal1 APN 1 72,655,660 (GRCm39) splice site probably null
IGL03306:Smarcal1 APN 1 72,665,625 (GRCm39) missense probably benign 0.12
R0133:Smarcal1 UTSW 1 72,672,010 (GRCm39) missense probably benign 0.05
R0315:Smarcal1 UTSW 1 72,634,970 (GRCm39) nonsense probably null
R0396:Smarcal1 UTSW 1 72,665,632 (GRCm39) missense probably benign 0.03
R0891:Smarcal1 UTSW 1 72,638,015 (GRCm39) missense probably damaging 0.99
R1799:Smarcal1 UTSW 1 72,625,120 (GRCm39) missense probably damaging 0.97
R1854:Smarcal1 UTSW 1 72,625,258 (GRCm39) missense possibly damaging 0.77
R3725:Smarcal1 UTSW 1 72,665,755 (GRCm39) missense possibly damaging 0.88
R3726:Smarcal1 UTSW 1 72,665,755 (GRCm39) missense possibly damaging 0.88
R4164:Smarcal1 UTSW 1 72,665,848 (GRCm39) intron probably benign
R4438:Smarcal1 UTSW 1 72,650,637 (GRCm39) intron probably benign
R4722:Smarcal1 UTSW 1 72,650,496 (GRCm39) missense probably damaging 1.00
R4796:Smarcal1 UTSW 1 72,636,599 (GRCm39) missense probably benign
R4989:Smarcal1 UTSW 1 72,672,019 (GRCm39) missense possibly damaging 0.84
R5242:Smarcal1 UTSW 1 72,630,242 (GRCm39) missense probably benign 0.00
R5367:Smarcal1 UTSW 1 72,635,135 (GRCm39) critical splice donor site probably null
R5418:Smarcal1 UTSW 1 72,638,068 (GRCm39) missense probably benign 0.01
R5430:Smarcal1 UTSW 1 72,665,776 (GRCm39) missense probably damaging 1.00
R5591:Smarcal1 UTSW 1 72,630,412 (GRCm39) missense probably damaging 1.00
R5607:Smarcal1 UTSW 1 72,625,372 (GRCm39) missense probably benign 0.00
R5809:Smarcal1 UTSW 1 72,630,296 (GRCm39) missense probably benign 0.09
R6395:Smarcal1 UTSW 1 72,655,716 (GRCm39) missense possibly damaging 0.82
R6447:Smarcal1 UTSW 1 72,625,033 (GRCm39) missense probably damaging 0.96
R6852:Smarcal1 UTSW 1 72,630,332 (GRCm39) missense possibly damaging 0.75
R7692:Smarcal1 UTSW 1 72,625,179 (GRCm39) missense probably benign 0.08
R7975:Smarcal1 UTSW 1 72,652,150 (GRCm39) missense probably benign 0.08
R8232:Smarcal1 UTSW 1 72,665,722 (GRCm39) missense probably damaging 1.00
R8407:Smarcal1 UTSW 1 72,640,554 (GRCm39) missense probably benign 0.04
R8901:Smarcal1 UTSW 1 72,624,939 (GRCm39) missense possibly damaging 0.71
R9329:Smarcal1 UTSW 1 72,665,697 (GRCm39) missense probably damaging 0.99
R9548:Smarcal1 UTSW 1 72,671,999 (GRCm39) missense possibly damaging 0.84
Z1177:Smarcal1 UTSW 1 72,630,426 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AGTACAGTCTGGAGACCCTAGG -3'
(R):5'- TTGGCTCCTCTTGCTCAAGG -3'

Sequencing Primer
(F):5'- TCTGGAGACCCTAGGCTAACAG -3'
(R):5'- TCCTCTTGCTCAAGGAGGCAG -3'
Posted On 2019-05-13