Incidental Mutation 'N/A - 293:Smarcad1'
ID 50
Institutional Source Beutler Lab
Gene Symbol Smarcad1
Ensembl Gene ENSMUSG00000029920
Gene Name SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1
Synonyms Etl1, D6Pas1
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.303) question?
Stock # N/A - 293 of strain aoba
Quality Score
Status Validated
Chromosome 6
Chromosomal Location 65019577-65093045 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 65051898 bp (GRCm39)
Zygosity Homozygous
Amino Acid Change Phenylalanine to Isoleucine at position 344 (F344I)
Ref Sequence ENSEMBL: ENSMUSP00000031984 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031984] [ENSMUST00000204620]
AlphaFold Q04692
Predicted Effect probably benign
Transcript: ENSMUST00000031984
AA Change: F344I

PolyPhen 2 Score 0.059 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000031984
Gene: ENSMUSG00000029920
AA Change: F344I

DomainStartEndE-ValueType
low complexity region 17 37 N/A INTRINSIC
low complexity region 39 53 N/A INTRINSIC
low complexity region 143 156 N/A INTRINSIC
low complexity region 210 224 N/A INTRINSIC
low complexity region 233 244 N/A INTRINSIC
low complexity region 333 348 N/A INTRINSIC
DEXDc 488 682 2.58e-38 SMART
Blast:DEXDc 685 745 4e-16 BLAST
HELICc 879 962 4.58e-21 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000203411
Predicted Effect noncoding transcript
Transcript: ENSMUST00000203756
Predicted Effect noncoding transcript
Transcript: ENSMUST00000204165
Predicted Effect noncoding transcript
Transcript: ENSMUST00000204420
Predicted Effect probably benign
Transcript: ENSMUST00000204620
SMART Domains Protein: ENSMUSP00000144767
Gene: ENSMUSG00000029920

DomainStartEndE-ValueType
low complexity region 17 37 N/A INTRINSIC
low complexity region 39 53 N/A INTRINSIC
Meta Mutation Damage Score 0.0693 question?
Coding Region Coverage
  • 1x: 88.4%
  • 3x: 74.0%
Validation Efficiency 85% (165/193)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the SNF subfamily of helicase proteins. The encoded protein plays a critical role in the restoration of heterochromatin organization and propagation of epigenetic patterns following DNA replication by mediating histone H3/H4 deacetylation. Mutations in this gene are associated with adermatoglyphia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit retarded growth, impaired fertility, skeletal dysplasias, and peri- and postnatal lethality. Mutant phenotypes are influenced by genetic background. [provided by MGI curators]
Allele List at MGI

All alleles(258) : Targeted, knock-out(1) Targeted, other(1) Gene trapped(256)

Other mutations in this stock
Total: 8 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Exoc1l T C 5: 76,664,339 (GRCm39) S143P probably benign Homo
Gm7634 T A 1: 16,124,084 (GRCm39) noncoding transcript Homo
Kras T A 6: 145,177,940 (GRCm39) M111L probably benign Homo
Lrig1 T C 6: 94,586,068 (GRCm39) T707A probably benign Homo
Mycbp2 A G 14: 103,461,898 (GRCm39) probably benign Homo
Or2a7 C T 6: 43,151,493 (GRCm39) T191I probably benign Homo
Sprr4 G A 3: 92,407,650 (GRCm39) Q51* probably null Homo
Zeb1 A T 18: 5,767,076 (GRCm39) H529L possibly damaging Homo
Other mutations in Smarcad1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02318:Smarcad1 APN 6 65,050,223 (GRCm39) missense probably damaging 1.00
IGL02707:Smarcad1 APN 6 65,029,790 (GRCm39) unclassified probably benign
IGL03006:Smarcad1 APN 6 65,060,873 (GRCm39) missense probably benign 0.01
IGL03131:Smarcad1 APN 6 65,051,937 (GRCm39) missense probably damaging 0.96
IGL03406:Smarcad1 APN 6 65,069,510 (GRCm39) missense probably damaging 0.98
Trollip UTSW 6 65,091,320 (GRCm39) missense probably damaging 1.00
wastrel UTSW 6 65,029,654 (GRCm39) missense probably damaging 1.00
R0020:Smarcad1 UTSW 6 65,060,991 (GRCm39) splice site probably benign
R0452:Smarcad1 UTSW 6 65,051,806 (GRCm39) missense possibly damaging 0.66
R1005:Smarcad1 UTSW 6 65,085,711 (GRCm39) missense probably benign 0.30
R1143:Smarcad1 UTSW 6 65,073,678 (GRCm39) missense probably benign 0.02
R1624:Smarcad1 UTSW 6 65,029,631 (GRCm39) missense probably benign 0.40
R1629:Smarcad1 UTSW 6 65,044,091 (GRCm39) missense probably benign 0.00
R1705:Smarcad1 UTSW 6 65,033,400 (GRCm39) missense probably damaging 1.00
R2000:Smarcad1 UTSW 6 65,050,200 (GRCm39) missense probably damaging 1.00
R2979:Smarcad1 UTSW 6 65,051,995 (GRCm39) missense probably benign 0.00
R3937:Smarcad1 UTSW 6 65,091,320 (GRCm39) missense probably damaging 1.00
R4391:Smarcad1 UTSW 6 65,033,443 (GRCm39) missense probably benign 0.17
R4648:Smarcad1 UTSW 6 65,044,073 (GRCm39) missense probably benign 0.04
R4697:Smarcad1 UTSW 6 65,029,625 (GRCm39) missense probably benign 0.00
R4709:Smarcad1 UTSW 6 65,052,099 (GRCm39) missense probably benign 0.01
R4726:Smarcad1 UTSW 6 65,052,025 (GRCm39) missense probably damaging 1.00
R4776:Smarcad1 UTSW 6 65,075,808 (GRCm39) missense probably null 1.00
R4928:Smarcad1 UTSW 6 65,051,898 (GRCm39) missense probably benign 0.06
R5619:Smarcad1 UTSW 6 65,088,865 (GRCm39) missense probably benign 0.03
R5709:Smarcad1 UTSW 6 65,051,746 (GRCm39) missense probably benign 0.01
R6038:Smarcad1 UTSW 6 65,050,232 (GRCm39) missense possibly damaging 0.91
R6038:Smarcad1 UTSW 6 65,050,232 (GRCm39) missense possibly damaging 0.91
R6220:Smarcad1 UTSW 6 65,091,313 (GRCm39) missense probably benign 0.09
R6302:Smarcad1 UTSW 6 65,052,122 (GRCm39) missense possibly damaging 0.93
R7014:Smarcad1 UTSW 6 65,029,654 (GRCm39) missense probably damaging 1.00
R7149:Smarcad1 UTSW 6 65,029,716 (GRCm39) missense probably benign 0.11
R7378:Smarcad1 UTSW 6 65,087,360 (GRCm39) missense probably benign 0.16
R7569:Smarcad1 UTSW 6 65,029,695 (GRCm39) missense probably benign 0.11
R7626:Smarcad1 UTSW 6 65,073,033 (GRCm39) missense possibly damaging 0.71
R7774:Smarcad1 UTSW 6 65,084,814 (GRCm39) missense probably damaging 1.00
R8079:Smarcad1 UTSW 6 65,029,766 (GRCm39) missense possibly damaging 0.51
R8119:Smarcad1 UTSW 6 65,071,303 (GRCm39) missense probably benign
R8129:Smarcad1 UTSW 6 65,044,078 (GRCm39) missense probably benign 0.09
R8558:Smarcad1 UTSW 6 65,060,908 (GRCm39) missense probably benign 0.09
R8679:Smarcad1 UTSW 6 65,088,865 (GRCm39) missense probably benign 0.03
R8770:Smarcad1 UTSW 6 65,029,718 (GRCm39) missense probably benign
R8795:Smarcad1 UTSW 6 65,049,033 (GRCm39) missense probably benign 0.10
R9104:Smarcad1 UTSW 6 65,075,649 (GRCm39) missense probably benign 0.06
R9133:Smarcad1 UTSW 6 65,049,035 (GRCm39) missense probably damaging 0.99
R9400:Smarcad1 UTSW 6 65,050,214 (GRCm39) missense probably damaging 0.97
R9401:Smarcad1 UTSW 6 65,071,321 (GRCm39) missense probably benign 0.00
R9608:Smarcad1 UTSW 6 65,091,318 (GRCm39) missense probably damaging 1.00
Nature of Mutation
DNA sequencing using the SOLiD technique identified a T to A transversion at position 1375 of the Smarcad1 transcript, in exon 9 of 24 total exons. The mutated nucleotide causes a phenylalanine to isoleucine substitution at amino acid 344 of the encoded protein. The mutation has been confirmed by DNA sequencing using the Sanger method (Figure 1).
Protein Function and Prediction
Smarcad1 encodes a 1021 amino acid ATP-dependent DNA helicase. The SMARCAD1 protein contains two CUE domains at residues 156-198 and 247-290 that may be involved in binding ubiquitin-conjugating enzymes, an ATP-binding helicase domain at amino acids 504-672, a C-terminal helicase domain with a DEAD box motif at residues 853-1005, and a nuclear localization signal at amino acids 716-733. The protein is phosphorylated on multiple residues (Uniprot Q04602). Homozygotes for a targeted null mutation exhibit retarded growth, impaired fertility, skeletal dysplasias, and peri- and postnatal lethality. Mutant phenotypes are influenced by genetic background. 
 
The F344I change does not occur in any of the SMARCAD1 domains, and is predicted to be possibly damaging by the PolyPhen program.
Posted On 2009-11-11