Incidental Mutation 'R7941:Syndig1'
ID 649041
Institutional Source Beutler Lab
Gene Symbol Syndig1
Ensembl Gene ENSMUSG00000074736
Gene Name synapse differentiation inducing 1
Synonyms Tmem90b, SynDIG1
MMRRC Submission 045987-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.099) question?
Stock # R7941 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 149672703-149846312 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 149741708 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Glutamic Acid at position 98 (V98E)
Ref Sequence ENSEMBL: ENSMUSP00000122327 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000109934] [ENSMUST00000109935] [ENSMUST00000137280] [ENSMUST00000140870] [ENSMUST00000144179] [ENSMUST00000149705]
AlphaFold A2ANU3
Predicted Effect probably benign
Transcript: ENSMUST00000109934
AA Change: V98E

PolyPhen 2 Score 0.366 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000105560
Gene: ENSMUSG00000074736
AA Change: V98E

DomainStartEndE-ValueType
Pfam:Dispanin 164 246 5.8e-27 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000109935
AA Change: V98E

PolyPhen 2 Score 0.366 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000105561
Gene: ENSMUSG00000074736
AA Change: V98E

DomainStartEndE-ValueType
low complexity region 151 171 N/A INTRINSIC
Pfam:CD225 172 244 7.9e-22 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000137280
Predicted Effect probably benign
Transcript: ENSMUST00000140870
Predicted Effect probably benign
Transcript: ENSMUST00000144179
Predicted Effect probably benign
Transcript: ENSMUST00000149705
AA Change: V98E

PolyPhen 2 Score 0.366 (Sensitivity: 0.90; Specificity: 0.89)
Meta Mutation Damage Score 0.1199 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 98.9%
Validation Efficiency 98% (43/44)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that belongs to the interferon-induced transmembrane family of proteins. A similar protein in rat is thought to regulate the development of excitatory synapses. [provided by RefSeq, Jul 2013]
Allele List at MGI
Other mutations in this stock
Total: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abl1 T C 2: 31,579,691 (GRCm39) probably benign Het
AI467606 A G 7: 126,691,593 (GRCm39) E56G probably damaging Het
Ak9 C T 10: 41,285,133 (GRCm39) P1403S unknown Het
Akr1c14 A G 13: 4,109,713 (GRCm39) K28E probably benign Het
Ampd2 C A 3: 107,987,432 (GRCm39) V134L probably benign Het
Anks1b A T 10: 90,413,017 (GRCm39) N55I probably damaging Het
Cabyr T C 18: 12,877,825 (GRCm39) L54P probably damaging Het
Cachd1 A T 4: 100,845,370 (GRCm39) N954I probably damaging Het
Cenpf A G 1: 189,389,483 (GRCm39) S1450P probably damaging Het
Chst10 T A 1: 38,910,772 (GRCm39) I131L probably damaging Het
Cluh A T 11: 74,550,583 (GRCm39) M270L probably benign Het
Dagla T C 19: 10,248,867 (GRCm39) H29R probably damaging Het
Dusp5 A G 19: 53,525,964 (GRCm39) N202S probably benign Het
Elavl3 A G 9: 21,947,612 (GRCm39) I110T possibly damaging Het
Fam222b G T 11: 78,045,885 (GRCm39) G482V possibly damaging Het
Fbxl7 A G 15: 26,543,699 (GRCm39) L316P probably damaging Het
Gad1 T A 2: 70,424,929 (GRCm39) probably null Het
H2-K2 T C 17: 34,218,305 (GRCm39) T204A probably benign Het
Hmcn1 A G 1: 150,525,835 (GRCm39) V3296A possibly damaging Het
Hyal1 T C 9: 107,455,299 (GRCm39) F203S probably damaging Het
Il16 T A 7: 83,332,037 (GRCm39) D181V probably damaging Het
Ip6k1 T C 9: 107,901,631 (GRCm39) F69L probably damaging Het
Klf4 G A 4: 55,531,755 (GRCm39) probably benign Het
Lsr T G 7: 30,672,520 (GRCm39) I27L probably benign Het
Mettl4 A T 17: 95,040,622 (GRCm39) probably null Het
Mpdz A G 4: 81,200,987 (GRCm39) V1902A probably benign Het
Nfkbiz C T 16: 55,642,307 (GRCm39) G37D probably damaging Het
Or5w11 T C 2: 87,459,248 (GRCm39) V31A probably benign Het
Otogl A T 10: 107,642,663 (GRCm39) probably null Het
Pcdh1 T C 18: 38,332,133 (GRCm39) D429G probably damaging Het
Pramel34 A T 5: 93,785,887 (GRCm39) V131D probably benign Het
Prelid2 A T 18: 42,065,816 (GRCm39) L73* probably null Het
Psg20 T A 7: 18,415,102 (GRCm39) probably null Het
Ptprb GAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACT GAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACT 10: 116,119,582 (GRCm39) probably benign Het
Rab24 C T 13: 55,468,120 (GRCm39) probably null Het
Rag1 T G 2: 101,472,691 (GRCm39) K817T probably benign Het
Rgl2 T C 17: 34,150,713 (GRCm39) V57A probably benign Het
Ric1 T C 19: 29,510,659 (GRCm39) M80T probably damaging Het
Sh3rf3 T C 10: 58,842,883 (GRCm39) I283T probably damaging Het
Skint2 C A 4: 112,483,187 (GRCm39) N197K probably damaging Het
Snapc4 A G 2: 26,266,730 (GRCm39) I126T probably damaging Het
Srcap GTCCTCCTCCTCCTCCTCCTGCTCCTCCTCCTCCTCCT GTCCTCCTCCTCCTCCTGCTCCTCCTCCTCCTCCT 7: 127,157,462 (GRCm39) probably benign Het
Svip T C 7: 51,653,161 (GRCm39) K51R probably benign Het
Tshz1 A T 18: 84,033,517 (GRCm39) M297K possibly damaging Het
Ttn A G 2: 76,749,694 (GRCm39) V3785A probably benign Het
Usf3 T C 16: 44,035,924 (GRCm39) S135P probably damaging Het
Vmn2r10 A T 5: 109,144,306 (GRCm39) M548K probably damaging Het
Vmn2r92 T C 17: 18,405,099 (GRCm39) S748P possibly damaging Het
Zbtb39 A G 10: 127,579,409 (GRCm39) Y661C probably damaging Het
Zfp804b A G 5: 6,820,042 (GRCm39) I1007T probably benign Het
Zscan4-ps2 A G 7: 11,251,599 (GRCm39) I212V probably benign Het
Other mutations in Syndig1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01506:Syndig1 APN 2 149,741,677 (GRCm39) missense probably damaging 1.00
IGL01599:Syndig1 APN 2 149,845,203 (GRCm39) missense probably damaging 1.00
IGL01814:Syndig1 APN 2 149,741,690 (GRCm39) missense probably damaging 1.00
IGL01988:Syndig1 APN 2 149,845,090 (GRCm39) splice site probably benign
IGL02323:Syndig1 APN 2 149,741,707 (GRCm39) missense probably benign 0.00
R1445:Syndig1 UTSW 2 149,772,841 (GRCm39) missense probably damaging 1.00
R1523:Syndig1 UTSW 2 149,845,154 (GRCm39) missense probably damaging 1.00
R4825:Syndig1 UTSW 2 149,741,473 (GRCm39) missense probably damaging 0.99
R4892:Syndig1 UTSW 2 149,741,811 (GRCm39) missense probably damaging 1.00
R5643:Syndig1 UTSW 2 149,741,428 (GRCm39) missense possibly damaging 0.78
R5644:Syndig1 UTSW 2 149,741,428 (GRCm39) missense possibly damaging 0.78
R6386:Syndig1 UTSW 2 149,741,496 (GRCm39) missense probably damaging 1.00
R6603:Syndig1 UTSW 2 149,845,208 (GRCm39) missense probably damaging 1.00
R8177:Syndig1 UTSW 2 149,741,788 (GRCm39) missense probably damaging 1.00
R9265:Syndig1 UTSW 2 149,845,160 (GRCm39) missense probably damaging 0.98
R9340:Syndig1 UTSW 2 149,845,175 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CCAGAAACTTCATGGCTGAGAG -3'
(R):5'- TGACCTCCAGCTCCTGTAAC -3'

Sequencing Primer
(F):5'- CTGAGAGCAGGGATGGTCTG -3'
(R):5'- TCCAGCTCCTGTAACTCCTC -3'
Posted On 2020-09-15