rs587777697
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PM4_Supporting
The NM_004170.6(SLC1A1):c.1184_1186delTCA(p.Ile395del) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,613,888 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as no classifications from unflagged records (no stars).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000024 ( 0 hom. )
Consequence
SLC1A1
NM_004170.6 disruptive_inframe_deletion
NM_004170.6 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.23
Publications
4 publications found
Genes affected
SLC1A1 (HGNC:10939): (solute carrier family 1 member 1) This gene encodes a member of the high-affinity glutamate transporters that play an essential role in transporting glutamate across plasma membranes. In brain, these transporters are crucial in terminating the postsynaptic action of the neurotransmitter glutamate, and in maintaining extracellular glutamate concentrations below neurotoxic levels. This transporter also transports aspartate, and mutations in this gene are thought to cause dicarboxylicamino aciduria, also known as glutamate-aspartate transport defect. [provided by RefSeq, Mar 2010]
SPATA6L (HGNC:25472): (spermatogenesis associated 6 like) Predicted to enable myosin light chain binding activity. Predicted to be involved in spermatogenesis. Predicted to be located in sperm connecting piece. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_004170.6. Strenght limited to Supporting due to length of the change: 1aa.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_004170.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SLC1A1 | NM_004170.6 | MANE Select | c.1184_1186delTCA | p.Ile395del | disruptive_inframe_deletion | Exon 10 of 12 | NP_004161.4 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SLC1A1 | ENST00000262352.8 | TSL:1 MANE Select | c.1184_1186delTCA | p.Ile395del | disruptive_inframe_deletion | Exon 10 of 12 | ENSP00000262352.3 | ||
| SLC1A1 | ENST00000931882.1 | c.1076_1078delTCA | p.Ile359del | disruptive_inframe_deletion | Exon 9 of 11 | ENSP00000601941.1 | |||
| SLC1A1 | ENST00000954075.1 | c.1043_1045delTCA | p.Ile348del | disruptive_inframe_deletion | Exon 9 of 11 | ENSP00000624134.1 |
Frequencies
GnomAD3 genomes 0.0000394 AC: 6AN: 152216Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
6
AN:
152216
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
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GnomAD2 exomes AF: 0.0000278 AC: 7AN: 251348 AF XY: 0.0000294 show subpopulations
GnomAD2 exomes
AF:
AC:
7
AN:
251348
AF XY:
Gnomad AFR exome
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GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461672Hom.: 0 AF XY: 0.0000193 AC XY: 14AN XY: 727130 show subpopulations
GnomAD4 exome
AF:
AC:
35
AN:
1461672
Hom.:
AF XY:
AC XY:
14
AN XY:
727130
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33472
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39698
South Asian (SAS)
AF:
AC:
1
AN:
86246
European-Finnish (FIN)
AF:
AC:
0
AN:
53420
Middle Eastern (MID)
AF:
AC:
0
AN:
5686
European-Non Finnish (NFE)
AF:
AC:
34
AN:
1111914
Other (OTH)
AF:
AC:
0
AN:
60376
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.461
Heterozygous variant carriers
0
2
4
7
9
11
0.00
0.20
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0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome 0.0000394 AC: 6AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74364 show subpopulations
GnomAD4 genome
AF:
AC:
6
AN:
152216
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
74364
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41454
American (AMR)
AF:
AC:
0
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5194
South Asian (SAS)
AF:
AC:
0
AN:
4824
European-Finnish (FIN)
AF:
AC:
0
AN:
10620
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
6
AN:
68044
Other (OTH)
AF:
AC:
0
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.533
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
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Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:no classifications from unflagged records
Revision:no classifications from unflagged records
Pathogenic
VUS
Benign
Condition
1
-
-
Dicarboxylic aminoaciduria (1)
1
-
-
Dicarboxylic aminoaciduria;C3808913:Schizophrenia 18 (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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