Incidental Mutation 'R0230:Hnf4a'
ID 34033
Institutional Source Beutler Lab
Gene Symbol Hnf4a
Ensembl Gene ENSMUSG00000017950
Gene Name hepatic nuclear factor 4, alpha
Synonyms Nuclear receptor 2A1, Nr2a1, HNF-4, Tcf4, MODY1, Hnf4, Tcf14, HNF4 alpha
MMRRC Submission 038473-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0230 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 163348731-163414827 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 163401005 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Serine at position 184 (F184S)
Ref Sequence ENSEMBL: ENSMUSP00000123511 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000018094] [ENSMUST00000109411] [ENSMUST00000137449]
AlphaFold P49698
Predicted Effect probably damaging
Transcript: ENSMUST00000018094
AA Change: F208S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000018094
Gene: ENSMUSG00000017950
AA Change: F208S

DomainStartEndE-ValueType
ZnF_C4 57 128 7.83e-38 SMART
HOLI 189 348 1.12e-47 SMART
low complexity region 383 393 N/A INTRINSIC
low complexity region 426 445 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000109411
AA Change: F199S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000105038
Gene: ENSMUSG00000017950
AA Change: F199S

DomainStartEndE-ValueType
ZnF_C4 48 119 7.83e-38 SMART
HOLI 180 339 1.12e-47 SMART
low complexity region 374 384 N/A INTRINSIC
low complexity region 417 436 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131658
Predicted Effect probably damaging
Transcript: ENSMUST00000137449
AA Change: F184S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000123511
Gene: ENSMUSG00000017950
AA Change: F184S

DomainStartEndE-ValueType
ZnF_C4 33 104 7.83e-38 SMART
Meta Mutation Damage Score 0.9590 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.7%
Validation Efficiency 100% (83/83)
MGI Phenotype FUNCTION: The protein encoded by this gene is a transcription factor involved in the development of the pancreas, liver, kidney, and intestines. The encoded protein also functions to maintain glucose homeostasis. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2015]
PHENOTYPE: Nullizygous embryos show delayed growth and lethality, impaired gastrulation, abnormal primitive streak and mesoderm formation, ectoderm apoptosis, and extraembryonic tissue dysplasia. Mice expressing only the alpha1 isoform show glucose intolerance whereas mice expressing alpha7 show dyslipidemia. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 80 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Amy1 T C 3: 113,352,079 (GRCm39) D371G probably benign Het
Asrgl1 T A 19: 9,095,883 (GRCm39) probably benign Het
Asxl3 T A 18: 22,585,383 (GRCm39) probably benign Het
B3galnt1 T C 3: 69,482,673 (GRCm39) N196S possibly damaging Het
Bbof1 A G 12: 84,471,978 (GRCm39) H74R probably damaging Het
Bpifb9b C T 2: 154,158,995 (GRCm39) T504M probably damaging Het
Cdk12 T G 11: 98,094,817 (GRCm39) S208R probably damaging Het
Cdk5r1 T C 11: 80,368,576 (GRCm39) L81P probably damaging Het
Chrd T C 16: 20,552,025 (GRCm39) L43P probably benign Het
Col6a4 A C 9: 105,949,565 (GRCm39) M690R probably benign Het
Cyp39a1 A T 17: 44,042,903 (GRCm39) R418W probably damaging Het
Dars2 C T 1: 160,890,357 (GRCm39) V162M probably benign Het
Dixdc1 C T 9: 50,606,807 (GRCm39) V270M possibly damaging Het
Dnah11 C A 12: 117,946,791 (GRCm39) E1194* probably null Het
Dnah7b T C 1: 46,258,508 (GRCm39) S1900P probably damaging Het
Dnah9 C T 11: 65,746,141 (GRCm39) E3991K probably damaging Het
Dsp A T 13: 38,381,681 (GRCm39) I2210F probably benign Het
Ebf1 A G 11: 44,886,949 (GRCm39) S556G probably damaging Het
Enam G A 5: 88,637,514 (GRCm39) probably benign Het
Eno1b T C 18: 48,180,806 (GRCm39) I328T probably benign Het
Epc1 T C 18: 6,440,168 (GRCm39) D579G probably damaging Het
Ephb3 A T 16: 21,039,525 (GRCm39) I426F probably damaging Het
Fam135b T G 15: 71,317,886 (GRCm39) I1359L probably benign Het
Fcgbpl1 T A 7: 27,856,250 (GRCm39) H2012Q probably damaging Het
Gm16519 T C 17: 71,236,128 (GRCm39) S26P probably benign Het
Gm17622 T A 13: 96,627,594 (GRCm39) probably null Het
Gpat2 G A 2: 127,277,765 (GRCm39) V764I possibly damaging Het
Gpx4 G A 10: 79,890,838 (GRCm39) A81T probably benign Het
Gss C A 2: 155,420,326 (GRCm39) R83L probably damaging Het
Hcls1 C A 16: 36,758,216 (GRCm39) Q36K probably damaging Het
Hepacam2 A G 6: 3,463,336 (GRCm39) V438A probably benign Het
Katnal1 T A 5: 148,855,460 (GRCm39) D90V possibly damaging Het
Kcnt2 A G 1: 140,174,083 (GRCm39) D30G probably benign Het
Kyat1 T C 2: 30,084,087 (GRCm39) E11G probably benign Het
Lefty1 T A 1: 180,764,579 (GRCm39) V168E probably damaging Het
Map2k6 C T 11: 110,387,281 (GRCm39) P218S probably damaging Het
Mlkl C G 8: 112,041,694 (GRCm39) K415N probably benign Het
Myh7 A T 14: 55,211,390 (GRCm39) M1593K probably benign Het
Myo19 T A 11: 84,784,159 (GRCm39) C186S possibly damaging Het
Ngp T C 9: 110,249,069 (GRCm39) L47P probably damaging Het
Nkiras1 A G 14: 18,280,185 (GRCm38) N192S probably benign Het
Or1j17 G A 2: 36,578,628 (GRCm39) V205M probably benign Het
Or2n1 A G 17: 38,486,841 (GRCm39) I289V probably damaging Het
Or2z8 C T 8: 72,812,244 (GRCm39) T240M probably damaging Het
Or8u9 T C 2: 86,001,886 (GRCm39) I92V probably benign Het
Pdcd6ip A G 9: 113,514,361 (GRCm39) probably benign Het
Pde4b T C 4: 102,454,707 (GRCm39) Y186H probably benign Het
Pex7 A G 10: 19,780,331 (GRCm39) V101A possibly damaging Het
Phldb3 G A 7: 24,312,004 (GRCm39) R106Q probably benign Het
Plxnc1 A G 10: 94,635,209 (GRCm39) V1339A probably benign Het
Proser1 A G 3: 53,386,383 (GRCm39) N755S probably damaging Het
Ptpn13 A G 5: 103,674,997 (GRCm39) D658G probably damaging Het
Rassf8 A C 6: 145,765,700 (GRCm39) probably benign Het
Rfc4 G A 16: 22,932,849 (GRCm39) Q363* probably null Het
Rxfp1 T C 3: 79,552,282 (GRCm39) N673S probably damaging Het
Scn7a T C 2: 66,556,628 (GRCm39) E319G probably damaging Het
Scnn1g A G 7: 121,345,984 (GRCm39) probably benign Het
Scube2 C T 7: 109,423,971 (GRCm39) probably null Het
Slc4a4 A C 5: 89,304,195 (GRCm39) H502P possibly damaging Het
Slc6a13 A G 6: 121,301,262 (GRCm39) N184D probably benign Het
Slco1a5 T A 6: 142,182,054 (GRCm39) probably benign Het
Slf1 T A 13: 77,260,867 (GRCm39) probably benign Het
Smarca4 G A 9: 21,612,168 (GRCm39) V1518I probably damaging Het
Smyd3 A G 1: 179,250,993 (GRCm39) probably benign Het
Sox5 A G 6: 144,155,064 (GRCm39) F11L probably benign Het
Spag17 T C 3: 100,014,143 (GRCm39) S2139P probably benign Het
Spice1 A T 16: 44,185,939 (GRCm39) probably benign Het
Sptan1 T A 2: 29,900,704 (GRCm39) probably benign Het
Srebf2 T A 15: 82,066,286 (GRCm39) N571K probably damaging Het
Tbl3 A G 17: 24,920,307 (GRCm39) L670P probably damaging Het
Tmem45a2 A G 16: 56,867,359 (GRCm39) V114A possibly damaging Het
Tmigd3 A G 3: 105,826,053 (GRCm39) N132D possibly damaging Het
Ttn T C 2: 76,567,778 (GRCm39) D19378G probably damaging Het
Ugcg C A 4: 59,189,739 (GRCm39) Y32* probably null Het
Ush2a C T 1: 188,582,301 (GRCm39) P3788L probably damaging Het
Usp22 T A 11: 61,050,023 (GRCm39) probably benign Het
Xaf1 T C 11: 72,197,381 (GRCm39) probably benign Het
Zbtb41 C T 1: 139,374,673 (GRCm39) T711I probably damaging Het
Zfp457 T C 13: 67,442,180 (GRCm39) T132A possibly damaging Het
Zfp64 T G 2: 168,754,150 (GRCm39) probably benign Het
Other mutations in Hnf4a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01393:Hnf4a APN 2 163,393,492 (GRCm39) splice site probably benign
IGL02077:Hnf4a APN 2 163,404,527 (GRCm39) critical splice donor site probably null
IGL02419:Hnf4a APN 2 163,408,202 (GRCm39) missense probably damaging 1.00
IGL02931:Hnf4a APN 2 163,408,037 (GRCm39) splice site probably benign
R1670:Hnf4a UTSW 2 163,404,496 (GRCm39) missense probably damaging 1.00
R1743:Hnf4a UTSW 2 163,408,259 (GRCm39) missense possibly damaging 0.65
R2131:Hnf4a UTSW 2 163,389,338 (GRCm39) missense probably benign 0.10
R2509:Hnf4a UTSW 2 163,408,161 (GRCm39) missense probably damaging 1.00
R4209:Hnf4a UTSW 2 163,410,809 (GRCm39) missense probably benign 0.00
R4737:Hnf4a UTSW 2 163,406,139 (GRCm39) missense probably benign 0.05
R5478:Hnf4a UTSW 2 163,410,926 (GRCm39) missense probably benign
R6382:Hnf4a UTSW 2 163,410,926 (GRCm39) missense probably benign
R7016:Hnf4a UTSW 2 163,406,193 (GRCm39) missense probably damaging 1.00
R7443:Hnf4a UTSW 2 163,400,932 (GRCm39) missense probably benign 0.03
R7875:Hnf4a UTSW 2 163,400,980 (GRCm39) nonsense probably null
R9189:Hnf4a UTSW 2 163,393,497 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- CACAGTCTAGCTGCCATCAGACAG -3'
(R):5'- ACAGGGGAGGTCCTTCTGAAATGC -3'

Sequencing Primer
(F):5'- ATGGGCTCTCTGTAAGGGAC -3'
(R):5'- gccccagtttccccacc -3'
Posted On 2013-05-09