Incidental Mutation 'R1799:Hltf'
ID 202904
Institutional Source Beutler Lab
Gene Symbol Hltf
Ensembl Gene ENSMUSG00000002428
Gene Name helicase-like transcription factor
Synonyms Snf2l3, Smarca3, P113
MMRRC Submission 039829-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1799 (G1)
Quality Score 225
Status Not validated
Chromosome 3
Chromosomal Location 20111975-20172654 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 20159855 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Histidine at position 702 (L702H)
Ref Sequence ENSEMBL: ENSMUSP00000002502 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000002502] [ENSMUST00000143005] [ENSMUST00000145853]
AlphaFold Q6PCN7
Predicted Effect probably damaging
Transcript: ENSMUST00000002502
AA Change: L702H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000002502
Gene: ENSMUSG00000002428
AA Change: L702H

DomainStartEndE-ValueType
HIRAN 60 154 3.78e-29 SMART
DEXDc 236 608 1.26e-32 SMART
RING 754 794 4.41e-6 SMART
low complexity region 814 828 N/A INTRINSIC
HELICc 859 944 2.24e-15 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000128127
Predicted Effect unknown
Transcript: ENSMUST00000143005
AA Change: F597I
SMART Domains Protein: ENSMUSP00000116570
Gene: ENSMUSG00000002428
AA Change: F597I

DomainStartEndE-ValueType
HIRAN 60 154 3.78e-29 SMART
DEXDc 236 610 2.36e-23 SMART
Predicted Effect unknown
Transcript: ENSMUST00000145853
AA Change: F535I
SMART Domains Protein: ENSMUSP00000118775
Gene: ENSMUSG00000002428
AA Change: F535I

DomainStartEndE-ValueType
HIRAN 1 92 2.7e-25 SMART
DEXDc 174 548 2.36e-23 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155635
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.] This gene encodes a member of the SWI/SNF family. 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 contains a RING finger DNA binding motif. Two transcript variants encoding the same protein have been found for this gene. However, use of an alternative translation start site produces an isoform that is truncated at the N-terminus compared to the full-length protein. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit neonatal lethality, spongiform encephalopathy with increased brain apoptosis, and hypoglycemia. Mice homozygous for a different knock-out allele fail to show fluoxetine-induced neurogenesis and behavioral responses. [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
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
Smarcal1 G T 1: 72,625,120 (GRCm39) C89F 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 Hltf
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00650:Hltf APN 3 20,159,796 (GRCm39) splice site probably benign
IGL01461:Hltf APN 3 20,154,103 (GRCm39) nonsense probably null
IGL01630:Hltf APN 3 20,137,068 (GRCm39) splice site probably benign
IGL01704:Hltf APN 3 20,137,910 (GRCm39) splice site probably benign
IGL02059:Hltf APN 3 20,160,621 (GRCm39) missense probably benign
IGL02105:Hltf APN 3 20,146,921 (GRCm39) missense probably damaging 1.00
IGL02156:Hltf APN 3 20,146,971 (GRCm39) missense possibly damaging 0.61
IGL02870:Hltf APN 3 20,154,037 (GRCm39) missense probably damaging 0.98
IGL02899:Hltf APN 3 20,153,981 (GRCm39) missense probably damaging 1.00
IGL02935:Hltf APN 3 20,123,215 (GRCm39) missense probably damaging 1.00
IGL02950:Hltf APN 3 20,130,736 (GRCm39) missense probably benign 0.07
IGL03082:Hltf APN 3 20,118,723 (GRCm39) splice site probably benign
snarky UTSW 3 20,163,651 (GRCm39) critical splice donor site probably null
R0068:Hltf UTSW 3 20,113,254 (GRCm39) missense probably damaging 1.00
R0787:Hltf UTSW 3 20,160,610 (GRCm39) missense probably damaging 1.00
R0905:Hltf UTSW 3 20,163,033 (GRCm39) critical splice donor site probably null
R0980:Hltf UTSW 3 20,145,665 (GRCm39) missense probably benign 0.00
R1741:Hltf UTSW 3 20,140,352 (GRCm39) missense probably damaging 1.00
R1748:Hltf UTSW 3 20,130,685 (GRCm39) missense probably benign 0.13
R1976:Hltf UTSW 3 20,160,610 (GRCm39) missense probably damaging 1.00
R2171:Hltf UTSW 3 20,113,245 (GRCm39) missense probably damaging 1.00
R2395:Hltf UTSW 3 20,146,906 (GRCm39) missense probably benign 0.41
R2444:Hltf UTSW 3 20,118,071 (GRCm39) missense possibly damaging 0.66
R3789:Hltf UTSW 3 20,123,211 (GRCm39) missense probably damaging 1.00
R3943:Hltf UTSW 3 20,146,908 (GRCm39) missense probably damaging 1.00
R4719:Hltf UTSW 3 20,118,865 (GRCm39) critical splice donor site probably null
R4793:Hltf UTSW 3 20,118,114 (GRCm39) missense possibly damaging 0.79
R5296:Hltf UTSW 3 20,162,276 (GRCm39) missense probably damaging 0.99
R5449:Hltf UTSW 3 20,123,247 (GRCm39) missense possibly damaging 0.92
R5492:Hltf UTSW 3 20,152,231 (GRCm39) splice site probably null
R6012:Hltf UTSW 3 20,113,098 (GRCm39) missense probably damaging 1.00
R6157:Hltf UTSW 3 20,130,660 (GRCm39) missense probably benign 0.13
R6254:Hltf UTSW 3 20,117,993 (GRCm39) missense possibly damaging 0.85
R6553:Hltf UTSW 3 20,126,558 (GRCm39) missense probably damaging 0.96
R6616:Hltf UTSW 3 20,163,651 (GRCm39) critical splice donor site probably null
R6696:Hltf UTSW 3 20,119,470 (GRCm39) splice site probably null
R6761:Hltf UTSW 3 20,137,996 (GRCm39) critical splice donor site probably null
R6781:Hltf UTSW 3 20,152,330 (GRCm39) missense probably benign 0.00
R7241:Hltf UTSW 3 20,119,556 (GRCm39) missense probably benign 0.07
R7356:Hltf UTSW 3 20,163,534 (GRCm39) missense probably damaging 1.00
R7453:Hltf UTSW 3 20,136,916 (GRCm39) missense possibly damaging 0.81
R7765:Hltf UTSW 3 20,145,647 (GRCm39) missense probably benign 0.02
R7978:Hltf UTSW 3 20,146,968 (GRCm39) missense probably damaging 1.00
R8299:Hltf UTSW 3 20,136,986 (GRCm39) missense possibly damaging 0.73
R8547:Hltf UTSW 3 20,152,291 (GRCm39) missense probably damaging 1.00
R8857:Hltf UTSW 3 20,159,825 (GRCm39) missense probably damaging 0.98
R8859:Hltf UTSW 3 20,119,566 (GRCm39) nonsense probably null
R8926:Hltf UTSW 3 20,123,323 (GRCm39) critical splice donor site probably null
R8959:Hltf UTSW 3 20,136,936 (GRCm39) missense probably damaging 1.00
R9052:Hltf UTSW 3 20,152,246 (GRCm39) missense probably damaging 1.00
R9214:Hltf UTSW 3 20,140,280 (GRCm39) missense probably benign 0.01
R9405:Hltf UTSW 3 20,137,094 (GRCm39) missense possibly damaging 0.88
R9565:Hltf UTSW 3 20,136,996 (GRCm39) critical splice donor site probably null
X0027:Hltf UTSW 3 20,121,553 (GRCm39) missense probably damaging 0.96
Predicted Primers PCR Primer
(F):5'- CAGCTGAGGTCTGTAGGTCATG -3'
(R):5'- ATGAAGGTACAATAGCCATCTCAC -3'

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