rs55671452
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2PM4
The NM_001160148.2(DDHD1):c.331_336delGGCGGC(p.Gly111_Gly112del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.00000421 in 1,425,980 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000042 ( 0 hom. )
Consequence
DDHD1
NM_001160148.2 conservative_inframe_deletion
NM_001160148.2 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.71
Publications
0 publications found
Genes affected
DDHD1 (HGNC:19714): (DDHD domain containing 1) This gene is a member of the intracellular phospholipase A1 gene family. The protein encoded by this gene preferentially hydrolyzes phosphatidic acid. It is a cytosolic protein with some mitochondrial localization, and is thought to be involved in the regulation of mitochondrial dynamics. Overexpression of this gene causes fragmentation of the tubular structures in mitochondria, while depletion of the gene results in mitochondrial tubule elongation. Deletion of this gene in male mice caused fertility defects, resulting from disruption in the organization of the mitochondria during spermiogenesis. In humans, mutations in this gene have been associated with hereditary spastic paraplegia (HSP), also known as Strumpell-Lorrain disease, or, familial spastic paraparesis (FSP). This inherited disorder is characterized by progressive weakness and spasticity of the legs. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_001160148.2.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001160148.2. 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 |
|---|---|---|---|---|---|---|---|---|---|
| DDHD1 | MANE Select | c.331_336delGGCGGC | p.Gly111_Gly112del | conservative_inframe_deletion | Exon 1 of 13 | NP_001153620.1 | Q8NEL9-1 | ||
| DDHD1 | c.331_336delGGCGGC | p.Gly111_Gly112del | conservative_inframe_deletion | Exon 1 of 13 | NP_001153619.1 | Q8NEL9-4 | |||
| DDHD1 | c.331_336delGGCGGC | p.Gly111_Gly112del | conservative_inframe_deletion | Exon 1 of 12 | NP_085140.2 | Q8NEL9-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DDHD1 | MANE Select | c.331_336delGGCGGC | p.Gly111_Gly112del | conservative_inframe_deletion | Exon 1 of 13 | ENSP00000500986.2 | Q8NEL9-1 | ||
| DDHD1 | TSL:1 | c.331_336delGGCGGC | p.Gly111_Gly112del | conservative_inframe_deletion | Exon 1 of 12 | ENSP00000350401.3 | Q8NEL9-2 | ||
| DDHD1 | c.331_336delGGCGGC | p.Gly111_Gly112del | conservative_inframe_deletion | Exon 1 of 15 | ENSP00000577235.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
0
GnomAD4 exome AF: 0.00000421 AC: 6AN: 1425980Hom.: 0 AF XY: 0.00000283 AC XY: 2AN XY: 707124 show subpopulations
GnomAD4 exome
AF:
AC:
6
AN:
1425980
Hom.:
AF XY:
AC XY:
2
AN XY:
707124
show subpopulations
African (AFR)
AF:
AC:
0
AN:
32884
American (AMR)
AF:
AC:
0
AN:
39264
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24980
East Asian (EAS)
AF:
AC:
0
AN:
38440
South Asian (SAS)
AF:
AC:
0
AN:
83114
European-Finnish (FIN)
AF:
AC:
0
AN:
49196
Middle Eastern (MID)
AF:
AC:
0
AN:
4600
European-Non Finnish (NFE)
AF:
AC:
6
AN:
1094614
Other (OTH)
AF:
AC:
0
AN:
58888
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.492
Heterozygous variant carriers
0
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2
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4
0.00
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome
GnomAD4 genome
Cov.:
0
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
Hereditary spastic paraplegia 28 (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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