chr1-1512412-C-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_001170535.3(ATAD3A):āc.144C>Gā(p.Ser48Arg) variant causes a missense change. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.0000067 ( 0 hom., cov: 29)
Exomes š: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ATAD3A
NM_001170535.3 missense
NM_001170535.3 missense
Scores
3
11
5
Clinical Significance
Conservation
PhyloP100: 6.87
Genes affected
ATAD3A (HGNC:25567): (ATPase family AAA domain containing 3A) This gene encodes a ubiquitously expressed mitochondrial membrane protein that contributes to mitochondrial dynamics, nucleoid organization, protein translation, cell growth, and cholesterol metabolism. This gene is a member of the ATPase family AAA-domain containing 3 gene family which, in humans, includes two other paralogs. Naturally occurring mutations in this gene are associated with distinct neurological syndromes including Harel-Yoon syndrome. High-level expression of this gene is associated with poor survival in breast cancer patients. A homozygous knockout of the orthologous gene in mice results in embryonic lethality at day 7.5 due to growth retardation and defective development of the trophoblast lineage. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATAD3A | NM_001170535.3 | c.144C>G | p.Ser48Arg | missense_variant | 1/16 | ENST00000378756.8 | NP_001164006.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATAD3A | ENST00000378756.8 | c.144C>G | p.Ser48Arg | missense_variant | 1/16 | 1 | NM_001170535.3 | ENSP00000368031 | P1 | |
ATAD3A | ENST00000378755.9 | c.144C>G | p.Ser48Arg | missense_variant | 1/16 | 2 | ENSP00000368030 | |||
ATAD3A | ENST00000672388.1 | n.248C>G | non_coding_transcript_exon_variant | 1/14 | ||||||
ATAD3A | ENST00000339113.9 | c.30C>G | p.Ser10Arg | missense_variant, NMD_transcript_variant | 1/17 | 2 | ENSP00000339421 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 149916Hom.: 0 Cov.: 29 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1080724Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 512580
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000667 AC: 1AN: 150016Hom.: 0 Cov.: 29 AF XY: 0.0000136 AC XY: 1AN XY: 73294
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 02, 2024 | The c.144C>G (p.S48R) alteration is located in exon 1 (coding exon 1) of the ATAD3A gene. This alteration results from a C to G substitution at nucleotide position 144, causing the serine (S) at amino acid position 48 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Pathogenic
D
MetaRNN
Uncertain
T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N
REVEL
Uncertain
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
1.0
.;D
Vest4
MutPred
Gain of MoRF binding (P = 0.0098);Gain of MoRF binding (P = 0.0098);
MVP
MPC
1.2
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.