Incidental Mutation 'R0543:Hnf1a'
ID 50048
Institutional Source Beutler Lab
Gene Symbol Hnf1a
Ensembl Gene ENSMUSG00000029556
Gene Name HNF1 homeobox A
Synonyms hepatocyte nuclear factor 1, Tcf1, HNF1, HNF1[a], Hnf-1, HNF1-alpha, LFB1, Hnf1alpha
MMRRC Submission 038735-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.865) question?
Stock # R0543 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 115087039-115109121 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 115088803 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Leucine at position 571 (S571L)
Ref Sequence ENSEMBL: ENSMUSP00000031535 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031535] [ENSMUST00000031538] [ENSMUST00000176550] [ENSMUST00000176911]
AlphaFold P22361
PDB Structure CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE DIMERIZATION DOMAIN OF HNF-1 ALPHA AND THE COACTIVATOR DCOH [X-RAY DIFFRACTION]
HNF-1ALPHA DIMERIZATION DOMAIN, WITH SELENOMETHIONINE SUBSTITUED AT LEU 12 [X-RAY DIFFRACTION]
DIMERIZATION DOMAIN OF HNF-1ALPHA WITH A LEU 13 SELENOMETHIONINE SUBSTITUTION [X-RAY DIFFRACTION]
WILD-TYPE HNF-1ALPHA DIMERIZATION DOMAIN [X-RAY DIFFRACTION]
Crystal Structure of Dimerization Domain (1-33) of HNF-1alpha [X-RAY DIFFRACTION]
Predicted Effect probably benign
Transcript: ENSMUST00000031535
AA Change: S571L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000031535
Gene: ENSMUSG00000029556
AA Change: S571L

DomainStartEndE-ValueType
Pfam:HNF-1_N 8 168 4e-57 PFAM
HOX 199 282 1.85e-7 SMART
low complexity region 288 297 N/A INTRINSIC
Blast:HOX 394 439 7e-20 BLAST
Pfam:HNF-1A_C 540 627 3.4e-38 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000031538
SMART Domains Protein: ENSMUSP00000031538
Gene: ENSMUSG00000029559

DomainStartEndE-ValueType
low complexity region 5 19 N/A INTRINSIC
low complexity region 40 52 N/A INTRINSIC
low complexity region 150 158 N/A INTRINSIC
low complexity region 182 206 N/A INTRINSIC
low complexity region 229 237 N/A INTRINSIC
low complexity region 240 255 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000131427
Predicted Effect probably benign
Transcript: ENSMUST00000131771
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140090
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147743
Predicted Effect probably benign
Transcript: ENSMUST00000176550
SMART Domains Protein: ENSMUSP00000135678
Gene: ENSMUSG00000029556

DomainStartEndE-ValueType
Pfam:HNF-1_N 1 176 4e-86 PFAM
Blast:HOX 199 238 2e-20 BLAST
SCOP:d1lfb__ 203 238 2e-18 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000176911
SMART Domains Protein: ENSMUSP00000135539
Gene: ENSMUSG00000029556

DomainStartEndE-ValueType
Pfam:HNF-1_N 1 118 6.4e-32 PFAM
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.5%
  • 20x: 93.3%
Validation Efficiency 99% (69/70)
MGI Phenotype FUNCTION: This gene encodes a hepatic transcription factor. The encoded protein is not a member of the T-cell factor family, and is distinct from T-cell specific transcription factor 7 which has also been referred to by the symbol Tcf1. [provided by RefSeq, Jul 2008]
PHENOTYPE: Most homozygous null mutants die at 3-6 weeks from progressive wasting syndrome, liver and renal dysfunction and type II diabetes. Mutants have little or no phenylalanine hydroxylase, albumin, alpha 1-antitrypsin and secreted insulin. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Alox5 T A 6: 116,431,278 (GRCm39) probably null Het
Apol9b A G 15: 77,619,840 (GRCm39) N212S probably damaging Het
Ash1l T A 3: 88,971,085 (GRCm39) probably null Het
Bltp1 G A 3: 37,050,607 (GRCm39) S2981N probably benign Het
Ccdc180 A T 4: 45,900,041 (GRCm39) K200* probably null Het
Ccser2 A T 14: 36,662,149 (GRCm39) M345K probably benign Het
Cdcp2 A T 4: 106,954,873 (GRCm39) probably null Het
Clca3a1 T C 3: 144,454,155 (GRCm39) probably benign Het
Cntn3 G A 6: 102,246,051 (GRCm39) probably benign Het
Col28a1 T A 6: 8,075,326 (GRCm39) probably benign Het
Dock2 A G 11: 34,244,325 (GRCm39) F1035S probably damaging Het
Dsg1a A T 18: 20,473,920 (GRCm39) S998C probably damaging Het
Ecrg4 C A 1: 43,781,449 (GRCm39) N110K possibly damaging Het
Enox1 T C 14: 77,744,399 (GRCm39) probably benign Het
Fgfr3 A G 5: 33,887,054 (GRCm39) M1V probably null Het
Fuca2 T A 10: 13,378,870 (GRCm39) Y5N probably damaging Het
Git2 G T 5: 114,883,592 (GRCm39) H42Q probably damaging Het
Gm7964 G A 7: 83,405,602 (GRCm39) noncoding transcript Het
Hars2 G A 18: 36,922,477 (GRCm39) E337K probably damaging Het
Hells A G 19: 38,956,194 (GRCm39) R797G probably benign Het
Hoxa5 T C 6: 52,181,320 (GRCm39) Y4C probably damaging Het
Inpp4a G A 1: 37,408,573 (GRCm39) probably benign Het
Ints6 T C 14: 62,934,060 (GRCm39) I816V probably damaging Het
Itpr1 T C 6: 108,492,709 (GRCm39) probably benign Het
Itprid2 T A 2: 79,474,850 (GRCm39) S270T possibly damaging Het
Kcnt2 C A 1: 140,537,352 (GRCm39) P1037T probably damaging Het
Lyg2 T A 1: 37,950,188 (GRCm39) M47L possibly damaging Het
Macf1 G T 4: 123,270,171 (GRCm39) A4648D probably damaging Het
Mcf2l T C 8: 13,046,728 (GRCm39) probably null Het
Mcm9 C T 10: 53,417,694 (GRCm39) R3H probably damaging Het
Met T A 6: 17,491,969 (GRCm39) Y244N probably damaging Het
Mettl14 A T 3: 123,168,411 (GRCm39) C210S possibly damaging Het
Mrgpra4 T C 7: 47,631,058 (GRCm39) Y181C probably benign Het
Mtch2 T C 2: 90,680,026 (GRCm39) V86A possibly damaging Het
Mttp A T 3: 137,817,457 (GRCm39) I446N possibly damaging Het
Muc4 T A 16: 32,577,120 (GRCm39) S2207T unknown Het
Muc5b A G 7: 141,405,522 (GRCm39) T944A unknown Het
Myo15a A T 11: 60,369,877 (GRCm39) H879L probably benign Het
Nherf4 A C 9: 44,160,231 (GRCm39) H324Q probably damaging Het
Nkiras2 G A 11: 100,515,018 (GRCm39) probably benign Het
Nostrin T G 2: 69,019,475 (GRCm39) *507E probably null Het
Nup205 T C 6: 35,175,904 (GRCm39) V589A probably benign Het
Or12j3 A G 7: 139,953,307 (GRCm39) I72T probably benign Het
Or5b21 G T 19: 12,839,252 (GRCm39) V38F probably benign Het
Or5w17 C A 2: 87,583,994 (GRCm39) L114F probably damaging Het
Oxct2b T A 4: 123,010,782 (GRCm39) M234K possibly damaging Het
Pcdha1 A T 18: 37,318,121 (GRCm39) I945F probably damaging Het
Pik3ca G A 3: 32,504,410 (GRCm39) probably null Het
Pkhd1l1 A G 15: 44,386,887 (GRCm39) probably null Het
Plscr1 A T 9: 92,140,099 (GRCm39) probably null Het
Prkn G A 17: 11,286,066 (GRCm39) D20N probably damaging Het
Psd T C 19: 46,307,956 (GRCm39) E684G possibly damaging Het
Rab11fip3 T C 17: 26,213,199 (GRCm39) E870G probably damaging Het
Rpl22l1 C A 3: 28,861,423 (GRCm39) Y103* probably null Het
Semp2l2b T C 10: 21,942,823 (GRCm39) S386G possibly damaging Het
Slc38a4 A T 15: 96,914,720 (GRCm39) N44K possibly damaging Het
Slco6c1 T A 1: 97,055,623 (GRCm39) I93F probably damaging Het
Strip1 G A 3: 107,534,091 (GRCm39) T181M possibly damaging Het
Stxbp5l G A 16: 37,028,458 (GRCm39) A535V probably damaging Het
Tg A T 15: 66,601,446 (GRCm39) Q152L probably benign Het
Thada T C 17: 84,730,591 (GRCm39) T1036A probably damaging Het
Tnfrsf21 C T 17: 43,349,104 (GRCm39) H239Y probably benign Het
Tns1 T A 1: 73,991,856 (GRCm39) T941S probably benign Het
Tppp3 T C 8: 106,194,840 (GRCm39) D97G probably benign Het
Trp53bp1 C A 2: 121,082,349 (GRCm39) A317S probably null Het
Trpm7 T C 2: 126,690,449 (GRCm39) I210V probably damaging Het
Ubr1 A G 2: 120,711,574 (GRCm39) L1440P probably damaging Het
Utp18 A T 11: 93,766,661 (GRCm39) Y317N probably damaging Het
Zdhhc5 T A 2: 84,522,824 (GRCm39) probably benign Het
Zfp719 A G 7: 43,238,677 (GRCm39) probably null Het
Other mutations in Hnf1a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01798:Hnf1a APN 5 115,091,732 (GRCm39) missense probably damaging 1.00
IGL02192:Hnf1a APN 5 115,098,177 (GRCm39) missense probably damaging 1.00
IGL03053:Hnf1a APN 5 115,108,792 (GRCm39) missense probably benign 0.00
R0522:Hnf1a UTSW 5 115,088,747 (GRCm39) splice site probably benign
R1498:Hnf1a UTSW 5 115,108,596 (GRCm39) missense probably damaging 1.00
R1827:Hnf1a UTSW 5 115,098,254 (GRCm39) missense probably damaging 1.00
R1852:Hnf1a UTSW 5 115,108,770 (GRCm39) missense probably damaging 1.00
R2408:Hnf1a UTSW 5 115,098,070 (GRCm39) splice site probably null
R2898:Hnf1a UTSW 5 115,098,106 (GRCm39) nonsense probably null
R4050:Hnf1a UTSW 5 115,108,633 (GRCm39) missense probably damaging 1.00
R4627:Hnf1a UTSW 5 115,093,930 (GRCm39) missense probably damaging 1.00
R4859:Hnf1a UTSW 5 115,093,311 (GRCm39) missense possibly damaging 0.84
R4873:Hnf1a UTSW 5 115,108,732 (GRCm39) missense probably benign 0.00
R4875:Hnf1a UTSW 5 115,108,732 (GRCm39) missense probably benign 0.00
R6488:Hnf1a UTSW 5 115,094,020 (GRCm39) missense probably benign
R7134:Hnf1a UTSW 5 115,091,446 (GRCm39) missense probably damaging 1.00
R7999:Hnf1a UTSW 5 115,098,233 (GRCm39) nonsense probably null
R8085:Hnf1a UTSW 5 115,108,732 (GRCm39) missense probably benign 0.00
R8093:Hnf1a UTSW 5 115,093,336 (GRCm39) missense probably benign
R8360:Hnf1a UTSW 5 115,091,391 (GRCm39) missense possibly damaging 0.93
R8539:Hnf1a UTSW 5 115,108,576 (GRCm39) critical splice donor site probably null
R9047:Hnf1a UTSW 5 115,088,882 (GRCm39) missense probably benign
X0067:Hnf1a UTSW 5 115,093,539 (GRCm39) missense possibly damaging 0.52
Z1176:Hnf1a UTSW 5 115,088,183 (GRCm39) frame shift probably null
Predicted Primers PCR Primer
(F):5'- CAAACTACTGCTTGGCATTCCGC -3'
(R):5'- GCAGACCATGTTGATCACAGACACC -3'

Sequencing Primer
(F):5'- CAGGCACCACATACAATGGG -3'
(R):5'- CTCAGCACCCTTGCCAG -3'
Posted On 2013-06-12