NM_177398.4:c.783_785delGCA
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3
The NM_177398.4(LMX1A):c.783_785delGCA(p.Gln262del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000172 in 1,439,146 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00017 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
LMX1A
NM_177398.4 disruptive_inframe_deletion
NM_177398.4 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.67
Publications
1 publications found
Genes affected
LMX1A (HGNC:6653): (LIM homeobox transcription factor 1 alpha) This gene encodes a homeodomain and LIM-domain containing protein. The encoded protein is a transcription factor that acts as a positive regulator of insulin gene transcription. This gene also plays a role in the development of dopamine producing neurons during embryogenesis. Mutations in this gene are associated with an increased risk of developing Parkinson's disease. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2012]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_177398.4
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_177398.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| LMX1A | NM_177398.4 | MANE Select | c.783_785delGCA | p.Gln262del | disruptive_inframe_deletion | Exon 7 of 9 | NP_796372.1 | Q8TE12-1 | |
| LMX1A | NM_001174069.2 | c.783_785delGCA | p.Gln262del | disruptive_inframe_deletion | Exon 7 of 9 | NP_001167540.1 | Q8TE12-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| LMX1A | ENST00000342310.7 | TSL:2 MANE Select | c.783_785delGCA | p.Gln262del | disruptive_inframe_deletion | Exon 7 of 9 | ENSP00000340226.3 | Q8TE12-1 | |
| LMX1A | ENST00000367893.4 | TSL:1 | c.783_785delGCA | p.Gln262del | disruptive_inframe_deletion | Exon 6 of 8 | ENSP00000356868.4 | Q8TE12-1 | |
| LMX1A | ENST00000489443.2 | TSL:1 | n.284_286delGCA | non_coding_transcript_exon | Exon 4 of 7 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152104Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152104
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
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Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
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Gnomad NFE
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Gnomad OTH
AF:
GnomAD2 exomes AF: 0.000413 AC: 98AN: 237208 AF XY: 0.000328 show subpopulations
GnomAD2 exomes
AF:
AC:
98
AN:
237208
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000172 AC: 247AN: 1439146Hom.: 0 AF XY: 0.000150 AC XY: 107AN XY: 715216 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
247
AN:
1439146
Hom.:
AF XY:
AC XY:
107
AN XY:
715216
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
5
AN:
32946
American (AMR)
AF:
AC:
8
AN:
43920
Ashkenazi Jewish (ASJ)
AF:
AC:
6
AN:
25618
East Asian (EAS)
AF:
AC:
6
AN:
39052
South Asian (SAS)
AF:
AC:
24
AN:
84104
European-Finnish (FIN)
AF:
AC:
31
AN:
52462
Middle Eastern (MID)
AF:
AC:
0
AN:
5684
European-Non Finnish (NFE)
AF:
AC:
160
AN:
1095982
Other (OTH)
AF:
AC:
7
AN:
59378
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.233
Heterozygous variant carriers
0
47
94
141
188
235
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
4
8
12
16
20
<30
30-35
35-40
40-45
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>80
Age
GnomAD4 genome 0.00000657 AC: 1AN: 152104Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74312 show subpopulations
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
152104
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
74312
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41432
American (AMR)
AF:
AC:
0
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5192
South Asian (SAS)
AF:
AC:
0
AN:
4830
European-Finnish (FIN)
AF:
AC:
0
AN:
10606
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67982
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational 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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