Incidental Mutation 'R4417:Matr3'
ID 326906
Institutional Source Beutler Lab
Gene Symbol Matr3
Ensembl Gene ENSMUSG00000037236
Gene Name matrin 3
Synonyms D030046F20Rik, 2810017I02Rik, 1110061A14Rik
MMRRC Submission 041138-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.959) question?
Stock # R4417 (G1)
Quality Score 225
Status Validated
Chromosome 18
Chromosomal Location 35695191-35726888 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 35705171 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Aspartic acid at position 32 (A32D)
Ref Sequence ENSEMBL: ENSMUSP00000140148 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000166793] [ENSMUST00000186292] [ENSMUST00000186614] [ENSMUST00000186796] [ENSMUST00000187389] [ENSMUST00000187513] [ENSMUST00000187543] [ENSMUST00000188359] [ENSMUST00000190029] [ENSMUST00000190458] [ENSMUST00000190121] [ENSMUST00000188275] [ENSMUST00000189039] [ENSMUST00000188767] [ENSMUST00000190653] [ENSMUST00000187793] [ENSMUST00000189163]
AlphaFold Q8K310
Predicted Effect probably damaging
Transcript: ENSMUST00000166793
AA Change: A32D

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000125761
Gene: ENSMUSG00000037236
AA Change: A32D

DomainStartEndE-ValueType
low complexity region 23 32 N/A INTRINSIC
low complexity region 52 65 N/A INTRINSIC
low complexity region 69 85 N/A INTRINSIC
ZnF_U1 288 322 4.47e-6 SMART
ZnF_C2H2 291 315 2.12e1 SMART
low complexity region 351 361 N/A INTRINSIC
low complexity region 371 386 N/A INTRINSIC
RRM 399 469 7.74e-3 SMART
RRM 497 567 5.63e-9 SMART
low complexity region 650 675 N/A INTRINSIC
low complexity region 710 718 N/A INTRINSIC
ZnF_U1 797 832 1.87e-8 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000186292
AA Change: A32D

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000139437
Gene: ENSMUSG00000037236
AA Change: A32D

DomainStartEndE-ValueType
low complexity region 23 32 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000186295
Predicted Effect probably damaging
Transcript: ENSMUST00000186614
AA Change: A32D

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000141189
Gene: ENSMUSG00000037236
AA Change: A32D

DomainStartEndE-ValueType
low complexity region 23 32 N/A INTRINSIC
low complexity region 52 65 N/A INTRINSIC
low complexity region 69 85 N/A INTRINSIC
ZnF_U1 288 322 2.6e-8 SMART
ZnF_C2H2 291 315 8.8e-2 SMART
low complexity region 351 361 N/A INTRINSIC
low complexity region 371 386 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000186796
SMART Domains Protein: ENSMUSP00000140128
Gene: ENSMUSG00000037236

DomainStartEndE-ValueType
low complexity region 13 23 N/A INTRINSIC
low complexity region 33 48 N/A INTRINSIC
RRM 61 131 3.2e-5 SMART
RRM 159 229 2.4e-11 SMART
low complexity region 312 337 N/A INTRINSIC
low complexity region 372 380 N/A INTRINSIC
ZnF_U1 459 494 1.1e-10 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000187389
AA Change: A32D

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000139745
Gene: ENSMUSG00000037236
AA Change: A32D

DomainStartEndE-ValueType
low complexity region 23 32 N/A INTRINSIC
low complexity region 52 65 N/A INTRINSIC
low complexity region 69 85 N/A INTRINSIC
ZnF_U1 288 322 4.47e-6 SMART
ZnF_C2H2 291 315 2.12e1 SMART
low complexity region 351 361 N/A INTRINSIC
low complexity region 371 386 N/A INTRINSIC
RRM 399 469 7.74e-3 SMART
RRM 497 567 5.63e-9 SMART
low complexity region 650 675 N/A INTRINSIC
low complexity region 710 718 N/A INTRINSIC
ZnF_U1 797 832 1.87e-8 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000187513
AA Change: A32D

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000139875
Gene: ENSMUSG00000099703
AA Change: A32D

DomainStartEndE-ValueType
low complexity region 23 32 N/A INTRINSIC
low complexity region 52 65 N/A INTRINSIC
low complexity region 69 85 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000187980
Predicted Effect unknown
Transcript: ENSMUST00000187543
AA Change: A32D
Predicted Effect probably damaging
Transcript: ENSMUST00000188359
AA Change: A32D

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000140148
Gene: ENSMUSG00000037236
AA Change: A32D

DomainStartEndE-ValueType
low complexity region 23 32 N/A INTRINSIC
low complexity region 52 65 N/A INTRINSIC
low complexity region 69 85 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000190029
AA Change: A32D

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000140846
Gene: ENSMUSG00000037236
AA Change: A32D

DomainStartEndE-ValueType
low complexity region 23 32 N/A INTRINSIC
low complexity region 52 65 N/A INTRINSIC
low complexity region 69 85 N/A INTRINSIC
ZnF_U1 288 322 4.47e-6 SMART
ZnF_C2H2 291 315 2.12e1 SMART
low complexity region 351 361 N/A INTRINSIC
low complexity region 371 386 N/A INTRINSIC
RRM 399 469 7.74e-3 SMART
RRM 497 567 5.63e-9 SMART
low complexity region 650 675 N/A INTRINSIC
low complexity region 710 718 N/A INTRINSIC
ZnF_U1 797 832 1.87e-8 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000190458
AA Change: A32D

PolyPhen 2 Score 0.958 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000139922
Gene: ENSMUSG00000099703
AA Change: A32D

DomainStartEndE-ValueType
low complexity region 23 32 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000190570
Predicted Effect noncoding transcript
Transcript: ENSMUST00000193225
Predicted Effect probably benign
Transcript: ENSMUST00000190121
SMART Domains Protein: ENSMUSP00000140853
Gene: ENSMUSG00000037236

DomainStartEndE-ValueType
low complexity region 13 23 N/A INTRINSIC
low complexity region 33 48 N/A INTRINSIC
RRM 61 131 3.2e-5 SMART
RRM 159 229 2.4e-11 SMART
low complexity region 312 337 N/A INTRINSIC
low complexity region 372 380 N/A INTRINSIC
ZnF_U1 459 494 1.1e-10 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000188275
SMART Domains Protein: ENSMUSP00000140401
Gene: ENSMUSG00000037236

DomainStartEndE-ValueType
low complexity region 63 73 N/A INTRINSIC
low complexity region 83 98 N/A INTRINSIC
RRM 111 181 3.2e-5 SMART
RRM 209 279 2.4e-11 SMART
low complexity region 362 387 N/A INTRINSIC
low complexity region 422 430 N/A INTRINSIC
ZnF_U1 509 544 1.1e-10 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000189039
SMART Domains Protein: ENSMUSP00000139525
Gene: ENSMUSG00000037236

DomainStartEndE-ValueType
ZnF_U1 36 70 2.6e-8 SMART
ZnF_C2H2 39 63 8.8e-2 SMART
low complexity region 99 109 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000188767
SMART Domains Protein: ENSMUSP00000141027
Gene: ENSMUSG00000037236

DomainStartEndE-ValueType
low complexity region 13 23 N/A INTRINSIC
low complexity region 33 48 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000190653
SMART Domains Protein: ENSMUSP00000141135
Gene: ENSMUSG00000037236

DomainStartEndE-ValueType
low complexity region 13 23 N/A INTRINSIC
low complexity region 33 48 N/A INTRINSIC
RRM 61 131 3.2e-5 SMART
RRM 159 229 2.4e-11 SMART
low complexity region 312 337 N/A INTRINSIC
low complexity region 372 380 N/A INTRINSIC
ZnF_U1 459 494 1.1e-10 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000187793
SMART Domains Protein: ENSMUSP00000140047
Gene: ENSMUSG00000099703

DomainStartEndE-ValueType
low complexity region 13 23 N/A INTRINSIC
SCOP:d1lvk_2 42 78 4e-3 SMART
PDB:1X4D|A 52 102 4e-30 PDB
Blast:RRM 61 102 1e-22 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000189163
Meta Mutation Damage Score 0.1925 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.5%
Validation Efficiency 100% (53/53)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a nuclear matrix protein, which is proposed to stabilize certain messenger RNA species. Mutations of this gene are associated with distal myopathy 2, which often includes vocal cord and pharyngeal weakness. Alternatively spliced transcript variants, including read-through transcripts composed of the upstream small nucleolar RNA host gene 4 (non-protein coding) and matrin 3 gene sequence, have been identified. Pseudogenes of this gene are located on chromosomes 1 and X. [provided by RefSeq, Aug 2013]
PHENOTYPE: Mice homozygous for a gene-trapped allele are early embryonic lethal. Heterozygotes show congenital heart defects including abnormal heart apex morphology, subaortic ventricular septal defects, double-outlet right ventricle, bicuspid aortic valve, aorta coarctation, and patent ductus arteriosus. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A630001G21Rik T A 1: 85,654,184 (GRCm39) Y51F probably damaging Het
Abi3bp C A 16: 56,474,398 (GRCm39) T631K probably damaging Het
BC004004 G A 17: 29,501,249 (GRCm39) probably benign Het
Cabp1 G A 5: 115,324,096 (GRCm39) S7L possibly damaging Het
Cdc23 ACC AC 18: 34,770,371 (GRCm39) probably null Het
Clhc1 T C 11: 29,521,826 (GRCm39) I453T possibly damaging Het
Col28a1 T A 6: 8,175,666 (GRCm39) I61F possibly damaging Het
Col2a1 T C 15: 97,896,466 (GRCm39) E61G unknown Het
Col6a4 C T 9: 105,949,215 (GRCm39) V807I probably damaging Het
Crhbp T C 13: 95,580,385 (GRCm39) S65G probably benign Het
Dnah9 T A 11: 65,872,040 (GRCm39) Q2730L possibly damaging Het
Epx T A 11: 87,760,256 (GRCm39) R453* probably null Het
Fez1 T C 9: 36,781,768 (GRCm39) probably benign Het
G530012D18Rik G C 1: 85,504,923 (GRCm39) probably benign Het
Glp2r T C 11: 67,555,342 (GRCm39) probably benign Het
Gpm6a T A 8: 55,503,223 (GRCm39) N157K probably damaging Het
Kcnj2 T C 11: 110,963,015 (GRCm39) S136P probably damaging Het
Lad1 A G 1: 135,756,484 (GRCm39) D364G probably benign Het
Lcp2 G T 11: 34,000,917 (GRCm39) E33D probably benign Het
Lrrc32 G T 7: 98,148,144 (GRCm39) R308L probably benign Het
Mfsd12 A G 10: 81,200,537 (GRCm39) probably benign Het
Mtmr11 T C 3: 96,075,207 (GRCm39) probably benign Het
Notch2 A G 3: 98,038,586 (GRCm39) D1243G possibly damaging Het
Odf2 T A 2: 29,805,333 (GRCm39) probably benign Het
Oit3 T C 10: 59,263,925 (GRCm39) Y403C probably damaging Het
Or4c125 T C 2: 89,170,331 (GRCm39) E105G probably benign Het
Pasd1 G A X: 70,983,225 (GRCm39) C399Y possibly damaging Het
Pitpnm2 G T 5: 124,261,632 (GRCm39) R977S probably damaging Het
Prdm13 T C 4: 21,678,756 (GRCm39) E578G probably benign Het
Pum3 A G 19: 27,400,116 (GRCm39) I183T probably damaging Het
Rdh14 G A 12: 10,441,231 (GRCm39) probably null Het
Slc35b2 G A 17: 45,877,355 (GRCm39) V161M probably benign Het
Slit1 A G 19: 41,602,908 (GRCm39) C968R probably damaging Het
Spag9 A T 11: 93,951,172 (GRCm39) probably benign Het
Spmip6 T C 4: 41,505,574 (GRCm39) T183A possibly damaging Het
Stox1 T C 10: 62,495,348 (GRCm39) N975S probably benign Het
Stradb T C 1: 59,033,531 (GRCm39) V398A probably benign Het
Tlr4 A T 4: 66,757,540 (GRCm39) N111I probably damaging Het
Tnip2 G A 5: 34,660,925 (GRCm39) R176* probably null Het
Tomm7 A G 5: 24,048,977 (GRCm39) I32T probably benign Het
Trank1 T C 9: 111,195,036 (GRCm39) I1020T probably benign Het
Ugt1a10 T G 1: 87,983,717 (GRCm39) S172A probably benign Het
Vmn2r115 T A 17: 23,564,854 (GRCm39) M247K probably benign Het
Zfp341 T C 2: 154,470,907 (GRCm39) L308P possibly damaging Het
Zmym6 T C 4: 126,986,781 (GRCm39) S154P probably damaging Het
Other mutations in Matr3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01396:Matr3 APN 18 35,721,442 (GRCm39) missense probably damaging 1.00
IGL03083:Matr3 APN 18 35,705,471 (GRCm39) missense probably damaging 0.96
IGL03117:Matr3 APN 18 35,705,710 (GRCm39) missense probably damaging 1.00
IGL03163:Matr3 APN 18 35,705,644 (GRCm39) missense probably damaging 0.99
IGL03381:Matr3 APN 18 35,712,078 (GRCm39) splice site probably benign
R0456:Matr3 UTSW 18 35,705,917 (GRCm39) missense probably damaging 1.00
R1136:Matr3 UTSW 18 35,705,948 (GRCm39) missense probably damaging 1.00
R1459:Matr3 UTSW 18 35,717,709 (GRCm39) missense probably benign 0.28
R1850:Matr3 UTSW 18 35,715,110 (GRCm39) missense probably damaging 1.00
R1929:Matr3 UTSW 18 35,721,378 (GRCm39) splice site probably benign
R2185:Matr3 UTSW 18 35,714,278 (GRCm39) missense probably damaging 1.00
R2366:Matr3 UTSW 18 35,721,448 (GRCm39) missense probably damaging 1.00
R2870:Matr3 UTSW 18 35,705,349 (GRCm39) missense probably benign 0.25
R2870:Matr3 UTSW 18 35,705,349 (GRCm39) missense probably benign 0.25
R2871:Matr3 UTSW 18 35,705,349 (GRCm39) missense probably benign 0.25
R2871:Matr3 UTSW 18 35,705,349 (GRCm39) missense probably benign 0.25
R2872:Matr3 UTSW 18 35,705,349 (GRCm39) missense probably benign 0.25
R2872:Matr3 UTSW 18 35,705,349 (GRCm39) missense probably benign 0.25
R2873:Matr3 UTSW 18 35,705,349 (GRCm39) missense probably benign 0.25
R3908:Matr3 UTSW 18 35,705,894 (GRCm39) missense probably damaging 1.00
R4400:Matr3 UTSW 18 35,716,969 (GRCm39) missense possibly damaging 0.80
R4860:Matr3 UTSW 18 35,714,693 (GRCm39) missense probably damaging 1.00
R4860:Matr3 UTSW 18 35,714,693 (GRCm39) missense probably damaging 1.00
R4881:Matr3 UTSW 18 35,705,428 (GRCm39) missense probably damaging 1.00
R4908:Matr3 UTSW 18 35,705,754 (GRCm39) missense probably damaging 0.96
R5084:Matr3 UTSW 18 35,715,135 (GRCm39) missense probably damaging 0.99
R5660:Matr3 UTSW 18 35,705,147 (GRCm39) missense probably damaging 0.99
R5709:Matr3 UTSW 18 35,715,015 (GRCm39) missense probably damaging 1.00
R5779:Matr3 UTSW 18 35,717,575 (GRCm39) missense possibly damaging 0.81
R5876:Matr3 UTSW 18 35,720,791 (GRCm39) missense probably benign
R6392:Matr3 UTSW 18 35,717,894 (GRCm39) missense probably benign 0.07
R7062:Matr3 UTSW 18 35,712,072 (GRCm39) critical splice donor site probably null
R7156:Matr3 UTSW 18 35,705,974 (GRCm39) missense probably damaging 0.98
R7228:Matr3 UTSW 18 35,695,537 (GRCm39) missense unknown
R7389:Matr3 UTSW 18 35,717,638 (GRCm39) missense probably benign
R8940:Matr3 UTSW 18 35,705,640 (GRCm39) missense probably damaging 0.98
R9071:Matr3 UTSW 18 35,705,803 (GRCm39) missense possibly damaging 0.94
R9159:Matr3 UTSW 18 35,712,355 (GRCm39) missense possibly damaging 0.71
R9205:Matr3 UTSW 18 35,720,774 (GRCm39) missense probably benign 0.08
R9587:Matr3 UTSW 18 35,717,876 (GRCm39) missense probably null 0.13
Predicted Primers PCR Primer
(F):5'- CAGCTTGAAGAAGATTCTACAGTCC -3'
(R):5'- GACAAAGGGAGTGGACCTCTAC -3'

Sequencing Primer
(F):5'- GGCGTTACCATTTTTGAAGCAAAG -3'
(R):5'- GGAGTGGACCTCTACTTCCAATG -3'
Posted On 2015-07-07