Incidental Mutation 'R2484:Chchd3'
ID 250811
Institutional Source Beutler Lab
Gene Symbol Chchd3
Ensembl Gene ENSMUSG00000053768
Gene Name coiled-coil-helix-coiled-coil-helix domain containing 3
Synonyms 1700039J09Rik, 0610041L09Rik, Micos19
MMRRC Submission 040408-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2484 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 32769142-33037206 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 32780950 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 184 (Y184H)
Ref Sequence ENSEMBL: ENSMUSP00000123220 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000066379] [ENSMUST00000124436] [ENSMUST00000127666] [ENSMUST00000129069]
AlphaFold Q9CRB9
Predicted Effect probably benign
Transcript: ENSMUST00000066379
AA Change: Y179H

PolyPhen 2 Score 0.179 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000070149
Gene: ENSMUSG00000053768
AA Change: Y179H

DomainStartEndE-ValueType
Pfam:DUF737 14 53 2.4e-16 PFAM
Pfam:DUF737 47 175 2.9e-36 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000124436
SMART Domains Protein: ENSMUSP00000138484
Gene: ENSMUSG00000053768

DomainStartEndE-ValueType
Pfam:DUF737 14 84 3e-25 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125264
Predicted Effect possibly damaging
Transcript: ENSMUST00000127666
AA Change: Y184H

PolyPhen 2 Score 0.465 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000123220
Gene: ENSMUSG00000053768
AA Change: Y184H

DomainStartEndE-ValueType
Pfam:DUF737 14 53 7.3e-17 PFAM
Pfam:DUF737 47 180 8.8e-40 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000129069
AA Change: Y41H

PolyPhen 2 Score 0.114 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000121589
Gene: ENSMUSG00000053768
AA Change: Y41H

DomainStartEndE-ValueType
Pfam:DUF737 1 37 2.9e-17 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129654
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133375
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140446
Predicted Effect noncoding transcript
Transcript: ENSMUST00000143206
Meta Mutation Damage Score 0.1795 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.5%
  • 20x: 95.7%
Validation Efficiency 97% (72/74)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is an inner mitochondrial membrane scaffold protein. Absence of the encoded protein affects the structural integrity of mitochondrial cristae and leads to reductions in ATP production, cell growth, and oxygen consumption. This protein is part of the mitochondrial contact site and cristae organizing system (MICOS). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]
PHENOTYPE: Mice homozygous for a transgenic gene disruption exhibit lethality prior to implantation. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 75 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4932414N04Rik G A 2: 68,541,819 (GRCm39) D46N possibly damaging Het
A830018L16Rik G T 1: 11,666,526 (GRCm39) A278S probably damaging Het
Acsbg3 A G 17: 57,189,641 (GRCm39) N252S probably benign Het
Adarb2 A T 13: 8,619,810 (GRCm39) K99* probably null Het
Arsi G A 18: 61,049,723 (GRCm39) G202E probably benign Het
Atxn1l A G 8: 110,458,883 (GRCm39) S460P probably damaging Het
Bicra T A 7: 15,722,605 (GRCm39) N304I possibly damaging Het
Capn10 A T 1: 92,872,565 (GRCm39) D470V probably damaging Het
Col6a6 T C 9: 105,658,003 (GRCm39) I736M probably damaging Het
Dhx36 T A 3: 62,380,236 (GRCm39) N820I probably damaging Het
Drd4 C T 7: 140,874,649 (GRCm39) P347S probably benign Het
Ephx1 A T 1: 180,817,537 (GRCm39) V378D probably damaging Het
Extl3 A T 14: 65,313,184 (GRCm39) V666E probably damaging Het
Fam20c G C 5: 138,794,872 (GRCm39) R500S probably benign Het
Glod4 A T 11: 76,130,344 (GRCm39) D42E probably damaging Het
Golga2 T C 2: 32,194,782 (GRCm39) I643T probably benign Het
Hnf1b A T 11: 83,752,661 (GRCm39) T73S probably benign Het
Hydin A G 8: 111,239,747 (GRCm39) Y2009C possibly damaging Het
Ido2 A G 8: 25,023,831 (GRCm39) C336R probably damaging Het
Ifngr1 T C 10: 19,477,163 (GRCm39) V108A probably damaging Het
Igbp1b A T 6: 138,634,492 (GRCm39) N317K probably benign Het
Ints14 A G 9: 64,893,366 (GRCm39) S511G probably benign Het
Itpr1 T C 6: 108,346,071 (GRCm39) S125P probably damaging Het
Jag1 T C 2: 136,926,620 (GRCm39) T975A possibly damaging Het
Klra17 A G 6: 129,845,720 (GRCm39) W165R probably damaging Het
Leo1 T A 9: 75,352,755 (GRCm39) N99K possibly damaging Het
Lonp1 C A 17: 56,921,659 (GRCm39) G883C probably damaging Het
Lpin1 C A 12: 16,597,500 (GRCm39) G682W probably damaging Het
Macf1 A C 4: 123,367,465 (GRCm39) L2432R probably damaging Het
Med12l T G 3: 59,205,259 (GRCm39) I2075M probably benign Het
Mroh6 A G 15: 75,756,177 (GRCm39) S660P probably benign Het
Myh6 G T 14: 55,198,699 (GRCm39) Y309* probably null Het
Myof C T 19: 37,892,291 (GRCm39) R1154H probably benign Het
Myrip G A 9: 120,253,685 (GRCm39) E253K probably benign Het
Ndst3 T C 3: 123,346,186 (GRCm39) D281G possibly damaging Het
Nipbl T C 15: 8,353,182 (GRCm39) K1788R probably damaging Het
Nol12 A G 15: 78,824,717 (GRCm39) probably benign Het
Nptn A G 9: 58,550,956 (GRCm39) T212A possibly damaging Het
Nptx2 C T 5: 144,493,155 (GRCm39) A414V probably damaging Het
Nub1 A G 5: 24,913,700 (GRCm39) D503G possibly damaging Het
Obscn T A 11: 58,898,366 (GRCm39) probably benign Het
Or4a80 A G 2: 89,582,578 (GRCm39) I198T probably benign Het
Or51q1 A G 7: 103,628,545 (GRCm39) T49A probably benign Het
Or5b97 C T 19: 12,879,005 (GRCm39) M46I probably benign Het
Pcnx2 T C 8: 126,617,859 (GRCm39) E132G probably damaging Het
Pkdcc A G 17: 83,529,667 (GRCm39) probably benign Het
Prdm2 T A 4: 142,861,776 (GRCm39) I505F probably damaging Het
Psmc3 C G 2: 90,886,346 (GRCm39) Q169E probably damaging Het
Ptger4 A T 15: 5,264,654 (GRCm39) I334N probably benign Het
Ptrh1 T C 2: 32,667,183 (GRCm39) M161T probably benign Het
Rapgef6 T A 11: 54,533,582 (GRCm39) V482D possibly damaging Het
Rdh16f2 T C 10: 127,710,946 (GRCm39) S188P probably damaging Het
Rrh T C 3: 129,616,040 (GRCm39) Y31C probably damaging Het
Selp G T 1: 163,971,523 (GRCm39) W659L probably benign Het
Selp G T 1: 163,971,524 (GRCm39) W659C probably damaging Het
Shh A G 5: 28,671,740 (GRCm39) C8R probably benign Het
Spdye4b C A 5: 143,187,848 (GRCm39) S167R possibly damaging Het
Strip1 T C 3: 107,535,537 (GRCm39) Y62C possibly damaging Het
Sucla2 A T 14: 73,819,149 (GRCm39) I232F probably benign Het
Sugp1 A G 8: 70,522,174 (GRCm39) D437G possibly damaging Het
Taf1a A G 1: 183,177,422 (GRCm39) probably benign Het
Tbc1d20 T A 2: 152,153,283 (GRCm39) M271K probably damaging Het
Tecpr2 T C 12: 110,899,752 (GRCm39) S707P probably benign Het
Tert G A 13: 73,796,104 (GRCm39) R1017H probably benign Het
Tox C G 4: 6,688,886 (GRCm39) V493L probably damaging Het
Tpo C T 12: 30,153,968 (GRCm39) A246T probably benign Het
Traf7 A T 17: 24,730,613 (GRCm39) V358D probably damaging Het
Trim56 C T 5: 137,141,528 (GRCm39) V663M possibly damaging Het
Unc80 C T 1: 66,560,740 (GRCm39) H823Y possibly damaging Het
Usf3 C T 16: 44,041,045 (GRCm39) H1842Y probably damaging Het
Uvrag T C 7: 98,537,668 (GRCm39) E509G probably benign Het
Vmn2r5 T C 3: 64,411,392 (GRCm39) D305G possibly damaging Het
Vmn2r52 T C 7: 9,903,058 (GRCm39) R457G probably damaging Het
Vti1a A C 19: 55,369,411 (GRCm39) N101T possibly damaging Het
Zfp236 A G 18: 82,686,762 (GRCm39) F259L probably benign Het
Other mutations in Chchd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00959:Chchd3 APN 6 32,945,188 (GRCm39) missense probably benign 0.16
IGL01153:Chchd3 APN 6 32,985,502 (GRCm39) splice site probably benign
IGL01347:Chchd3 APN 6 32,780,838 (GRCm39) missense probably benign 0.04
R0580:Chchd3 UTSW 6 32,870,325 (GRCm39) critical splice donor site probably null
R1438:Chchd3 UTSW 6 32,985,503 (GRCm39) splice site probably benign
R2294:Chchd3 UTSW 6 32,829,122 (GRCm39) missense probably damaging 1.00
R5122:Chchd3 UTSW 6 32,945,240 (GRCm39) missense probably benign 0.08
R7502:Chchd3 UTSW 6 32,945,164 (GRCm39) missense probably damaging 0.97
R8927:Chchd3 UTSW 6 32,780,951 (GRCm39) missense probably benign 0.00
R8928:Chchd3 UTSW 6 32,780,951 (GRCm39) missense probably benign 0.00
R9233:Chchd3 UTSW 6 32,780,845 (GRCm39) missense probably damaging 1.00
R9517:Chchd3 UTSW 6 33,026,317 (GRCm39) missense probably benign 0.06
Predicted Primers PCR Primer
(F):5'- GAGAAAGTTTCCCACCCACTGG -3'
(R):5'- AGATCTTCATGGCCTGCTG -3'

Sequencing Primer
(F):5'- CACTGGGATGACTGGGCTTTCTAC -3'
(R):5'- TGGCCATGGGTATGCCAG -3'
Posted On 2014-12-04