Incidental Mutation 'R1799:Smarcal1'
ID 202885
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 039829-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1799 (G1)
Quality Score 198
Status Not validated
Chromosome 1
Chromosomal Location 72622410-72672293 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 72625120 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Phenylalanine at position 89 (C89F)
Ref Sequence ENSEMBL: ENSMUSP00000120230 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047615] [ENSMUST00000133123] [ENSMUST00000145868] [ENSMUST00000152225]
AlphaFold Q8BJL0
Predicted Effect probably benign
Transcript: ENSMUST00000047615
AA Change: C89F

PolyPhen 2 Score 0.243 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000047589
Gene: ENSMUSG00000039354
AA Change: C89F

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 benign
Transcript: ENSMUST00000133123
SMART Domains Protein: ENSMUSP00000114848
Gene: ENSMUSG00000039354

DomainStartEndE-ValueType
low complexity region 31 51 N/A INTRINSIC
Pfam:HARP 66 106 1.7e-14 PFAM
Pfam:HARP 140 194 2.2e-28 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000136498
Predicted Effect probably damaging
Transcript: ENSMUST00000145868
AA Change: C89F

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000120230
Gene: ENSMUSG00000039354
AA Change: C89F

DomainStartEndE-ValueType
low complexity region 31 51 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000150725
Predicted Effect probably benign
Transcript: ENSMUST00000152225
AA Change: C89F

PolyPhen 2 Score 0.243 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000137833
Gene: ENSMUSG00000039354
AA Change: C89F

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156797
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152814
Coding Region Coverage
  • 1x: 97.5%
  • 3x: 96.9%
  • 10x: 95.3%
  • 20x: 92.3%
Validation Efficiency
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: 102 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A930011G23Rik A G 5: 99,382,435 (GRCm39) L271P probably benign Het
Adamts3 A C 5: 89,923,280 (GRCm39) D175E probably benign Het
Adcy4 T C 14: 56,008,929 (GRCm39) T833A probably benign Het
Adgrf5 A T 17: 43,750,958 (GRCm39) I508F probably damaging Het
Arhgap9 G T 10: 127,163,593 (GRCm39) V464L probably damaging Het
Atp10a T A 7: 58,474,182 (GRCm39) D1156E probably damaging Het
Atp2a1 A T 7: 126,049,314 (GRCm39) M576K probably benign Het
Atrx T C X: 104,891,235 (GRCm39) Q1536R probably damaging Het
Ccdc141 A C 2: 76,842,015 (GRCm39) V1472G possibly damaging Het
Cd84 A G 1: 171,700,317 (GRCm39) T145A possibly damaging Het
Celsr1 G T 15: 85,916,886 (GRCm39) N362K probably damaging Het
Cep290 G A 10: 100,352,058 (GRCm39) A755T probably benign Het
Cfap70 T A 14: 20,445,067 (GRCm39) E1071V probably damaging Het
Cps1 T C 1: 67,248,801 (GRCm39) V1176A probably damaging Het
Csf2rb2 A C 15: 78,181,268 (GRCm39) N41K probably damaging Het
Csn1s2a G A 5: 87,926,052 (GRCm39) V43M probably damaging Het
Cyp26b1 T C 6: 84,561,254 (GRCm39) D136G probably benign Het
Cyp7b1 A G 3: 18,151,616 (GRCm39) L199P probably benign Het
Dapk1 C T 13: 60,867,468 (GRCm39) T225I probably damaging Het
Dio2 T A 12: 90,696,680 (GRCm39) T103S probably benign Het
Dipk1a C A 5: 108,057,713 (GRCm39) V237F probably damaging Het
Dnhd1 T A 7: 105,304,974 (GRCm39) S339T probably benign Het
Drc1 A G 5: 30,523,841 (GRCm39) N737D probably damaging Het
Efhc1 C T 1: 21,049,762 (GRCm39) P541S probably benign Het
Elmo2 A T 2: 165,134,077 (GRCm39) I637N probably damaging Het
Eps15 T A 4: 109,240,034 (GRCm39) D492E probably damaging Het
Ermn G T 2: 57,938,249 (GRCm39) N121K probably benign Het
F5 A G 1: 164,021,100 (GRCm39) T1192A possibly damaging Het
Fbxo22 T C 9: 55,130,771 (GRCm39) F347L probably benign Het
Fbxw15 G A 9: 109,387,314 (GRCm39) S227F probably damaging Het
Foxj3 A G 4: 119,476,548 (GRCm39) N242S probably benign Het
Gjb3 G A 4: 127,220,224 (GRCm39) R103W probably damaging Het
Grm4 A G 17: 27,691,914 (GRCm39) V235A probably damaging Het
Gstm4 T C 3: 107,950,874 (GRCm39) N74S probably damaging Het
Gtf3c3 A G 1: 54,459,583 (GRCm39) V393A possibly damaging Het
Hltf T A 3: 20,159,855 (GRCm39) L702H probably damaging Het
Inpp4a T A 1: 37,432,059 (GRCm39) V153E possibly damaging Het
Kmt5c T C 7: 4,745,729 (GRCm39) probably null Het
Kynu A G 2: 43,494,169 (GRCm39) R201G possibly damaging Het
Lrp2 T A 2: 69,333,874 (GRCm39) T1456S probably benign Het
Lrrc40 G A 3: 157,742,441 (GRCm39) V19I probably benign Het
M1ap T A 6: 82,982,491 (GRCm39) C258* probably null Het
Man2a1 T C 17: 65,059,452 (GRCm39) L1113P probably benign Het
Man2a1 C T 17: 64,976,492 (GRCm39) R427W probably damaging Het
Meikin C A 11: 54,308,613 (GRCm39) Q404K probably benign Het
Mfsd4a T C 1: 131,981,334 (GRCm39) I222V possibly damaging Het
N4bp2 A G 5: 65,964,168 (GRCm39) N739S possibly damaging Het
Ncoa2 A T 1: 13,232,517 (GRCm39) probably null Het
Nisch G T 14: 30,899,228 (GRCm39) probably benign Het
Nmur2 A G 11: 55,920,447 (GRCm39) V266A probably damaging Het
Npcd G A 15: 79,712,987 (GRCm39) R147C probably damaging Het
Or4q3 T A 14: 50,583,537 (GRCm39) M121L probably benign Het
Or5ac25 T A 16: 59,182,243 (GRCm39) I113F probably benign Het
Pals2 T A 6: 50,173,525 (GRCm39) M463K probably damaging Het
Parp4 A T 14: 56,885,589 (GRCm39) H1556L unknown Het
Pcdh9 G T 14: 94,126,107 (GRCm39) A21E probably benign Het
Phtf1 A G 3: 103,903,958 (GRCm39) E436G probably benign Het
Piezo2 C A 18: 63,165,911 (GRCm39) probably null Het
Piezo2 T C 18: 63,241,158 (GRCm39) Y690C probably damaging Het
Pla2g4f T C 2: 120,141,549 (GRCm39) R183G possibly damaging Het
Plxnd1 T C 6: 115,971,018 (GRCm39) D250G probably damaging Het
Ppig A G 2: 69,579,744 (GRCm39) D426G unknown Het
Ppp3cb T C 14: 20,574,540 (GRCm39) E185G possibly damaging Het
Qsox1 A T 1: 155,670,364 (GRCm39) M151K probably null Het
Ralgapa2 T C 2: 146,184,648 (GRCm39) E1453G probably benign Het
Rnf167 G A 11: 70,540,838 (GRCm39) V191I probably benign Het
Rp1 T C 1: 4,419,055 (GRCm39) K686E possibly damaging Het
Ryr1 T G 7: 28,767,046 (GRCm39) Q2979P probably damaging Het
Scaf1 T A 7: 44,657,443 (GRCm39) I479F probably damaging Het
Septin8 A G 11: 53,425,310 (GRCm39) T68A probably benign Het
Sh3rf1 A T 8: 61,825,661 (GRCm39) N552I probably damaging Het
Shoc1 A T 4: 59,099,383 (GRCm39) V103D possibly damaging Het
Slc1a3 A G 15: 8,717,888 (GRCm39) L68P probably damaging Het
Slc39a6 G A 18: 24,718,524 (GRCm39) P511L probably benign Het
Slc9c1 A G 16: 45,374,652 (GRCm39) Y339C probably damaging Het
Smu1 A T 4: 40,745,537 (GRCm39) M261K probably damaging Het
Spag8 T G 4: 43,653,087 (GRCm39) probably benign Het
Spag8 T C 4: 43,653,345 (GRCm39) probably benign Het
Spata31d1a T C 13: 59,851,216 (GRCm39) D304G probably benign Het
Spdl1 A T 11: 34,711,856 (GRCm39) L298* probably null Het
Stac2 C T 11: 97,930,444 (GRCm39) probably null Het
Stag1 A G 9: 100,835,515 (GRCm39) probably null Het
Stpg2 C T 3: 139,125,542 (GRCm39) P445L probably damaging Het
Sult2a8 A T 7: 14,157,451 (GRCm39) V128E probably damaging Het
Synm A G 7: 67,385,707 (GRCm39) F210L probably damaging Het
Tbck C G 3: 132,480,263 (GRCm39) A714G probably benign Het
Tcerg1 A T 18: 42,694,012 (GRCm39) Y711F possibly damaging Het
Tnfrsf25 A G 4: 152,201,465 (GRCm39) T98A probably benign Het
Togaram2 T C 17: 71,998,450 (GRCm39) S218P probably damaging Het
Tpp1 A T 7: 105,399,515 (GRCm39) D84E probably benign Het
Trim30d G T 7: 104,132,682 (GRCm39) Q202K probably damaging Het
Trim37 T A 11: 87,068,845 (GRCm39) V397E probably damaging Het
Triml1 A T 8: 43,583,512 (GRCm39) I363N probably damaging Het
Trpm6 T A 19: 18,869,363 (GRCm39) probably null Het
Tsc2 T C 17: 24,823,382 (GRCm39) S1055G probably benign Het
Ubr5 T C 15: 37,989,621 (GRCm39) D2065G probably damaging Het
Uggt2 G T 14: 119,269,688 (GRCm39) P948Q probably benign Het
Vps13c A T 9: 67,851,399 (GRCm39) S2345C probably damaging Het
Wtap G T 17: 13,199,771 (GRCm39) R48S possibly damaging Het
Zbtb38 A G 9: 96,570,934 (GRCm39) V50A probably damaging Het
Zcchc2 T A 1: 105,958,017 (GRCm39) S829R probably benign Het
Zfp385b T C 2: 77,246,316 (GRCm39) D237G probably benign 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
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
R7060:Smarcal1 UTSW 1 72,652,101 (GRCm39) missense probably damaging 1.00
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'- TGTCAGAACAGCCACAGAGC -3'
(R):5'- GTCCGAAATGCTCTGCCTAG -3'

Sequencing Primer
(F):5'- TCTCCTGAATCTCCTAGCG -3'
(R):5'- TTGGCCTCTAACTCGGGGTC -3'
Posted On 2014-06-23