Incidental Mutation 'R3764:Hadha'
ID 271804
Institutional Source Beutler Lab
Gene Symbol Hadha
Ensembl Gene ENSMUSG00000025745
Gene Name hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha
Synonyms Mtpa
MMRRC Submission 040741-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R3764 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 30324421-30359978 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 30349207 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Glutamic Acid at position 135 (K135E)
Ref Sequence ENSEMBL: ENSMUSP00000120976 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000156859]
AlphaFold Q8BMS1
Predicted Effect noncoding transcript
Transcript: ENSMUST00000026843
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130358
Predicted Effect probably damaging
Transcript: ENSMUST00000156859
AA Change: K135E

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000120976
Gene: ENSMUSG00000025745
AA Change: K135E

DomainStartEndE-ValueType
Pfam:ECH_1 44 297 3.6e-42 PFAM
Pfam:ECH_2 49 225 8.6e-27 PFAM
Pfam:3HCDH_N 363 542 1e-54 PFAM
Pfam:3HCDH 544 639 7.7e-29 PFAM
low complexity region 706 720 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000197491
Predicted Effect noncoding transcript
Transcript: ENSMUST00000199559
Meta Mutation Damage Score 0.4186 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.5%
  • 20x: 92.3%
Validation Efficiency 100% (29/29)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the alpha subunit of the mitochondrial trifunctional protein, which catalyzes the last three steps of mitochondrial beta-oxidation of long chain fatty acids. The mitochondrial membrane-bound heterocomplex is composed of four alpha and four beta subunits, with the alpha subunit catalyzing the 3-hydroxyacyl-CoA dehydrogenase and enoyl-CoA hydratase activities. Mutations in this gene result in trifunctional protein deficiency or LCHAD deficiency. The genes of the alpha and beta subunits of the mitochondrial trifunctional protein are located adjacent to each other in the human genome in a head-to-head orientation. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for disruptions in this gene die within 36 hours with hypoglycemia and liver steatosis. Liver steatosis and insulin resistance develop in heterozygotes with age. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 25 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Afdn G A 17: 14,066,851 (GRCm39) A648T probably benign Het
Cadm3 C T 1: 173,174,064 (GRCm39) V50I probably damaging Het
Catspere2 A T 1: 177,940,698 (GRCm39) T687S unknown Het
Cubn T A 2: 13,336,396 (GRCm39) I2477F possibly damaging Het
Ddx41 G A 13: 55,682,293 (GRCm39) R205W possibly damaging Het
Dhx15 G A 5: 52,324,074 (GRCm39) P406L probably benign Het
Eif4e3 C T 6: 99,617,586 (GRCm39) R95Q probably damaging Het
Fmo5 T C 3: 97,553,033 (GRCm39) I327T probably damaging Het
Gckr T A 5: 31,483,842 (GRCm39) probably benign Het
Ghrhr T C 6: 55,357,756 (GRCm39) V129A probably damaging Het
Gsdma A T 11: 98,561,593 (GRCm39) N191I probably damaging Het
Hjurp GT GTT 1: 88,194,246 (GRCm39) probably null Het
Lrp2 T C 2: 69,326,680 (GRCm39) E1797G probably damaging Het
Ly9 T C 1: 171,421,712 (GRCm39) Y513C possibly damaging Het
Nphp4 C T 4: 152,622,474 (GRCm39) probably benign Het
Pate8 A T 9: 36,493,114 (GRCm39) probably null Het
Pcm1 A G 8: 41,783,919 (GRCm39) E2005G probably damaging Het
Spsb2 T C 6: 124,786,518 (GRCm39) Y84H probably damaging Het
Tlcd3b T C 7: 126,426,685 (GRCm39) I36T probably damaging Het
Try10 C T 6: 41,333,458 (GRCm39) R68C probably benign Het
Tut7 T A 13: 59,948,194 (GRCm39) E307V probably damaging Het
Ube3c ACTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT ACTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCT 5: 29,842,584 (GRCm39) probably benign Het
Vps50 A T 6: 3,588,063 (GRCm39) I679F probably damaging Het
Wdr81 G A 11: 75,343,629 (GRCm39) T546I probably damaging Het
Zfp40 T A 17: 23,396,101 (GRCm39) H94L possibly damaging Het
Other mutations in Hadha
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00430:Hadha APN 5 30,325,145 (GRCm39) missense possibly damaging 0.94
IGL00435:Hadha APN 5 30,327,171 (GRCm39) missense probably benign 0.12
IGL01413:Hadha APN 5 30,346,025 (GRCm39) missense probably benign 0.01
IGL01715:Hadha APN 5 30,325,082 (GRCm39) missense probably damaging 1.00
IGL02065:Hadha APN 5 30,347,843 (GRCm39) splice site probably benign
IGL02316:Hadha APN 5 30,331,565 (GRCm39) missense probably benign 0.04
IGL02366:Hadha APN 5 30,340,048 (GRCm39) missense probably benign 0.01
IGL02453:Hadha APN 5 30,349,304 (GRCm39) splice site probably benign
IGL02611:Hadha APN 5 30,333,941 (GRCm39) splice site probably benign
IGL03127:Hadha APN 5 30,339,184 (GRCm39) splice site probably benign
IGL03181:Hadha APN 5 30,326,524 (GRCm39) missense probably benign 0.20
R1381:Hadha UTSW 5 30,333,834 (GRCm39) missense probably benign
R1501:Hadha UTSW 5 30,333,804 (GRCm39) missense probably benign 0.02
R2060:Hadha UTSW 5 30,333,834 (GRCm39) missense probably benign 0.30
R3778:Hadha UTSW 5 30,325,127 (GRCm39) missense probably damaging 0.98
R5025:Hadha UTSW 5 30,359,959 (GRCm39) unclassified probably benign
R5523:Hadha UTSW 5 30,350,252 (GRCm39) missense possibly damaging 0.78
R5870:Hadha UTSW 5 30,349,284 (GRCm39) missense possibly damaging 0.61
R6054:Hadha UTSW 5 30,328,682 (GRCm39) missense probably benign 0.00
R6144:Hadha UTSW 5 30,345,994 (GRCm39) missense probably benign 0.04
R6245:Hadha UTSW 5 30,325,042 (GRCm39) critical splice donor site probably null
R6495:Hadha UTSW 5 30,325,048 (GRCm39) missense probably benign 0.03
R6862:Hadha UTSW 5 30,352,977 (GRCm39) critical splice donor site probably null
R7038:Hadha UTSW 5 30,324,998 (GRCm39) splice site probably null
R7200:Hadha UTSW 5 30,350,315 (GRCm39) missense probably benign 0.25
R7215:Hadha UTSW 5 30,324,840 (GRCm39) missense probably benign 0.00
R7267:Hadha UTSW 5 30,327,755 (GRCm39) missense probably damaging 1.00
R7414:Hadha UTSW 5 30,331,610 (GRCm39) missense possibly damaging 0.95
R8172:Hadha UTSW 5 30,350,285 (GRCm39) missense probably damaging 0.97
R8429:Hadha UTSW 5 30,349,255 (GRCm39) missense probably benign 0.00
R8494:Hadha UTSW 5 30,347,810 (GRCm39) missense probably damaging 1.00
R8516:Hadha UTSW 5 30,331,582 (GRCm39) missense probably damaging 1.00
R9180:Hadha UTSW 5 30,340,038 (GRCm39) missense probably benign
R9618:Hadha UTSW 5 30,339,165 (GRCm39) missense possibly damaging 0.73
Predicted Primers PCR Primer
(F):5'- AACCATTCAGGCATTTGACAG -3'
(R):5'- TGTGTTTGAAGACTCATTGCC -3'

Sequencing Primer
(F):5'- GGCATTTGACAGCTGAAAATAAAATC -3'
(R):5'- GTTTGAAGACTCATTGCCAAATATTG -3'
Genotyping

Genotyping is performed by amplifying the region containing the mutation using PCR, followed by sequencing of the amplified region to detect the mutation.

PCR Primers

R37640010_PCR_F: 5’- AACCATTCAGGCATTTGACAG-3’

R37640010_PCR_R: 5’- TGTGTTTGAAGACTCATTGCC-3’

Sequencing Primers

R37640010_SEQ_F: 5’- GGCATTTGACAGCTGAAAATAAAATC-3’
 

R37640010_SEQ_R: 5’- GTTTGAAGACTCATTGCCAAATATTG-3’
 

PCR program

1) 94°C             2:00

2) 94°C             0:30

3) 55°C             0:30

4) 72°C             1:00

5) repeat steps (2-4) 40X

6) 72°C             10:00

7) 4°C               hold

The following sequence of 412 nucleotides is amplified (NCBI RefSeq: NC_000071, chromosome 5:30144014-30144425):

aaccattcag gcatttgaca gctgaaaata aaatcacttc tactcagaaa actgttcttt

tgctgttttt aggtaaaacg gtagcctaaa gggctctggt ggcagtgagt gggaaagcct     

gaacagctct ggaatacttc tatacctcaa gtcctcctcc caagcaggat ccactgatgg      

cggccacaac gggctttggg gacttttcaa gtttctcaaa cattctctga ccttcctgtg      

atattcgtgt tgcttcttgg ggggttgtac aagaggatag catgctgcag tatcgacaga      

aaagaaaaac acaaaaggag agatgagact gtggcctatt ttgtataata tttcacccac      

tatatactta tctcaatgta tatcaatatt tggcaatgag tcttcaaaca ca

Primer binding sites are underlined and the sequencing primer is highlighted; the mutated nucleotide is shown in red text (Chr. (+) = T>C).
Posted On 2015-03-25