Incidental Mutation 'R1976:Hltf'
ID 221680
Institutional Source Beutler Lab
Gene Symbol Hltf
Ensembl Gene ENSMUSG00000002428
Gene Name helicase-like transcription factor
Synonyms Snf2l3, Smarca3, P113
MMRRC Submission 039989-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1976 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 20111975-20172654 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 20160610 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 759 (D759G)
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: D759G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000002502
Gene: ENSMUSG00000002428
AA Change: D759G

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155635
Meta Mutation Damage Score 0.3005 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.8%
Validation Efficiency 98% (65/66)
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: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca13 T C 11: 9,347,815 (GRCm39) V3556A probably damaging Het
Abcb5 T C 12: 118,854,417 (GRCm39) I833V probably benign Het
Adgrd1 A T 5: 129,217,861 (GRCm39) H432L probably benign Het
Alppl2 T A 1: 87,016,463 (GRCm39) I204F probably damaging Het
Ascc3 T A 10: 50,525,262 (GRCm39) F486I probably damaging Het
Bcl9l T A 9: 44,417,449 (GRCm39) L429Q possibly damaging Het
Ccdc33 A T 9: 58,024,445 (GRCm39) Y227* probably null Het
Cd101 A G 3: 100,915,377 (GRCm39) V730A probably damaging Het
Cdadc1 A T 14: 59,811,217 (GRCm39) V431E probably damaging Het
Dazap1 T A 10: 80,110,454 (GRCm39) probably null Het
Dbpht2 T A 12: 74,342,635 (GRCm39) noncoding transcript Het
Dennd4b A T 3: 90,180,362 (GRCm39) T742S probably damaging Het
Dhtkd1 T C 2: 5,907,202 (GRCm39) E838G possibly damaging Het
Dync2h1 A T 9: 7,129,045 (GRCm39) D1823E probably benign Het
Enox1 T A 14: 77,906,233 (GRCm39) N556K probably benign Het
Fam227a T C 15: 79,510,477 (GRCm39) I392M possibly damaging Het
Fnip2 A T 3: 79,388,238 (GRCm39) M831K probably benign Het
Foxn1 T C 11: 78,256,763 (GRCm39) probably benign Het
Garre1 A C 7: 33,956,805 (GRCm39) N353K probably damaging Het
Glis3 T C 19: 28,240,077 (GRCm39) 936 probably benign Het
Gm4953 T A 1: 158,995,923 (GRCm39) noncoding transcript Het
Gsr T G 8: 34,170,288 (GRCm39) probably null Het
Habp4 G T 13: 64,332,420 (GRCm39) V344F probably benign Het
Hdac7 G A 15: 97,704,386 (GRCm39) Q495* probably null Het
Helb T C 10: 119,930,168 (GRCm39) D737G possibly damaging Het
Hlx G T 1: 184,464,184 (GRCm39) A52D probably damaging Het
Itga10 C T 3: 96,559,054 (GRCm39) probably benign Het
Itsn2 A G 12: 4,722,733 (GRCm39) probably benign Het
Kank2 A T 9: 21,705,857 (GRCm39) V387E probably damaging Het
Lefty1 T C 1: 180,765,389 (GRCm39) V319A probably benign Het
Lonp1 T C 17: 56,922,068 (GRCm39) T771A possibly damaging Het
Lpcat2b A T 5: 107,581,716 (GRCm39) K348N possibly damaging Het
Lsamp T C 16: 41,709,430 (GRCm39) V103A probably damaging Het
Ltbp4 A T 7: 27,026,195 (GRCm39) C538S probably damaging Het
Micu1 T C 10: 59,604,035 (GRCm39) S174P probably damaging Het
Mta1 A G 12: 113,099,926 (GRCm39) N607S probably damaging Het
Muc5b C T 7: 141,416,891 (GRCm39) S3279L probably benign Het
Naalad2 T C 9: 18,289,995 (GRCm39) E211G probably damaging Het
Nup155 T A 15: 8,165,311 (GRCm39) M649K probably benign Het
Pan2 T C 10: 128,156,282 (GRCm39) V1171A probably damaging Het
Pisd A G 5: 32,896,209 (GRCm39) V372A probably damaging Het
Prim1 T A 10: 127,859,668 (GRCm39) C288S probably benign Het
Rab23 T A 1: 33,763,019 (GRCm39) C30S probably damaging Het
Sacs A G 14: 61,440,344 (GRCm39) T797A probably benign Het
Sall3 T C 18: 81,015,108 (GRCm39) D940G probably benign Het
Scn1a T C 2: 66,161,615 (GRCm39) E311G probably benign Het
Sdk1 T A 5: 142,129,573 (GRCm39) I1598N probably damaging Het
Slc22a17 A T 14: 55,145,957 (GRCm39) probably null Het
Slc36a4 T A 9: 15,645,506 (GRCm39) V311D probably damaging Het
Sprr3 T A 3: 92,364,253 (GRCm39) Q197L possibly damaging Het
Stab2 A C 10: 86,732,360 (GRCm39) probably null Het
Stk4 C T 2: 163,942,448 (GRCm39) T360M probably benign Het
Tas2r123 T A 6: 132,824,295 (GRCm39) V64D probably damaging Het
Trhde T G 10: 114,424,336 (GRCm39) N483T possibly damaging Het
Trp53 C T 11: 69,479,323 (GRCm39) T167M probably damaging Het
Tspan8 A G 10: 115,680,035 (GRCm39) I217V probably benign Het
Tut4 T C 4: 108,336,720 (GRCm39) L148P probably benign Het
Usp17la A G 7: 104,509,527 (GRCm39) E44G possibly damaging Het
Usp40 T G 1: 87,906,258 (GRCm39) Q659P probably benign Het
Vmn1r4 T C 6: 56,933,723 (GRCm39) C76R probably damaging Het
Vmn2r118 C T 17: 55,899,925 (GRCm39) G660R probably damaging Het
Zfp786 T A 6: 47,796,691 (GRCm39) H749L probably damaging 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
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'- GGCATGATTTCTGCAAATACCAG -3'
(R):5'- TATCATCTCTGGAACGTGGC -3'

Sequencing Primer
(F):5'- TAGGAAGTGACACGCCTG -3'
(R):5'- AACGTGGCTGGGTTTTTATTATACC -3'
Posted On 2014-08-25