Incidental Mutation 'R5492:Hltf'
ID 432110
Institutional Source Beutler Lab
Gene Symbol Hltf
Ensembl Gene ENSMUSG00000002428
Gene Name helicase-like transcription factor
Synonyms Snf2l3, Smarca3, P113
MMRRC Submission 043053-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5492 (G1)
Quality Score 225
Status Not validated
Chromosome 3
Chromosomal Location 20111975-20172654 bp(+) (GRCm39)
Type of Mutation splice site
DNA Base Change (assembly) T to A at 20152231 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000002502 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000002502] [ENSMUST00000143005] [ENSMUST00000145853]
AlphaFold Q6PCN7
Predicted Effect probably null
Transcript: ENSMUST00000002502
SMART Domains Protein: ENSMUSP00000002502
Gene: ENSMUSG00000002428

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 probably benign
Transcript: ENSMUST00000143005
SMART Domains Protein: ENSMUSP00000116570
Gene: ENSMUSG00000002428

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

DomainStartEndE-ValueType
HIRAN 1 92 2.7e-25 SMART
DEXDc 174 548 2.36e-23 SMART
Coding Region Coverage
  • 1x: 98.2%
  • 3x: 97.1%
  • 10x: 94.5%
  • 20x: 89.3%
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: 37 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A830018L16Rik C T 1: 11,615,431 (GRCm39) R135C probably damaging Het
Abcd2 A G 15: 91,073,176 (GRCm39) Y328H probably benign Het
Abcg4 T C 9: 44,189,355 (GRCm39) T381A probably benign Het
Adamts12 A G 15: 11,336,384 (GRCm39) N1490D probably benign Het
Aldh18a1 C T 19: 40,539,734 (GRCm39) R747Q probably damaging Het
Armc8 G T 9: 99,409,184 (GRCm39) C169* probably null Het
Birc6 A C 17: 74,977,369 (GRCm39) N4388T probably damaging Het
Bsn G A 9: 107,989,714 (GRCm39) P2013S probably damaging Het
Cdc16 A G 8: 13,813,915 (GRCm39) probably null Het
Cmtr1 T A 17: 29,909,316 (GRCm39) F408L probably damaging Het
Col4a2 C T 8: 11,488,608 (GRCm39) R1104W possibly damaging Het
Drg2 A C 11: 60,352,422 (GRCm39) H208P probably damaging Het
Frem3 A T 8: 81,339,306 (GRCm39) D533V probably damaging Het
Gm9930 T A 10: 9,410,337 (GRCm39) noncoding transcript Het
Haus5 A G 7: 30,358,380 (GRCm39) V305A possibly damaging Het
Hint3 C A 10: 30,494,245 (GRCm39) R30L probably benign Het
Hmcn2 T A 2: 31,310,318 (GRCm39) L3304Q probably benign Het
Hspa2 A G 12: 76,451,308 (GRCm39) M1V probably null Het
Htr5b T C 1: 121,455,387 (GRCm39) T178A possibly damaging Het
Ighv1-11 A G 12: 114,576,084 (GRCm39) S44P probably damaging Het
Larp1b C T 3: 40,924,334 (GRCm39) R104W probably damaging Het
Map3k2 A G 18: 32,361,189 (GRCm39) T550A probably damaging Het
Map4 T A 9: 109,881,450 (GRCm39) S105T possibly damaging Het
Mgam T C 6: 40,733,297 (GRCm39) C691R probably damaging Het
Mms19 A G 19: 41,944,270 (GRCm39) I310T possibly damaging Het
Myh2 A C 11: 67,071,701 (GRCm39) K506T probably benign Het
Ngdn T C 14: 55,260,509 (GRCm39) V239A probably benign Het
Plin1 G A 7: 79,375,460 (GRCm39) R151* probably null Het
Rbpjl GCC GC 2: 164,256,330 (GRCm39) probably null Het
Rdh16f2 G T 10: 127,702,623 (GRCm39) E67* probably null Het
Slc25a36 A C 9: 96,982,259 (GRCm39) C25W probably damaging Het
Stk31 G A 6: 49,375,177 (GRCm39) A49T probably damaging Het
Tigar T A 6: 127,066,167 (GRCm39) T124S possibly damaging Het
Tsn A G 1: 118,232,443 (GRCm39) V144A probably damaging Het
Zfp703 C T 8: 27,469,233 (GRCm39) P299L probably damaging Het
Zfp943 T A 17: 22,212,056 (GRCm39) C381S probably damaging Het
Zfyve19 A T 2: 119,039,595 (GRCm39) 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
R1799:Hltf UTSW 3 20,159,855 (GRCm39) missense probably damaging 1.00
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
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'- GCTCAGTGTGTCAAACATTTGC -3'
(R):5'- ATCGTCACTAATGGATCACCTC -3'

Sequencing Primer
(F):5'- AACCTTAGTTAGCCTGGGCCTAG -3'
(R):5'- TGGATCACCTCATAAACTTACTTACC -3'
Posted On 2016-10-05