chr11-112016758-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001037954.4(DIXDC1):c.1824C>A(p.Asp608Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. D608D) has been classified as Benign.
Frequency
Genomes: not found (cov: 31)
Consequence
DIXDC1
NM_001037954.4 missense
NM_001037954.4 missense
Scores
1
9
6
Clinical Significance
Conservation
PhyloP100: 1.20
Genes affected
DIXDC1 (HGNC:23695): (DIX domain containing 1) The protein encoded by this gene is a positive regulator of the Wnt signaling pathway. The encoded protein is found associated with gamma tubulin at the centrosome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jun 2013]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIXDC1 | NM_001037954.4 | c.1824C>A | p.Asp608Glu | missense_variant | 18/20 | ENST00000440460.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIXDC1 | ENST00000440460.7 | c.1824C>A | p.Asp608Glu | missense_variant | 18/20 | 1 | NM_001037954.4 | P1 | |
DIXDC1 | ENST00000615255.1 | c.1191C>A | p.Asp397Glu | missense_variant | 14/16 | 1 | |||
DIXDC1 | ENST00000526500.5 | n.820C>A | non_coding_transcript_exon_variant | 9/11 | 2 | ||||
DIXDC1 | ENST00000618522.4 | n.1177C>A | non_coding_transcript_exon_variant | 12/14 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome ? Cov.: 31
GnomAD4 genome
?
Cov.:
31
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2021 | The c.1824C>A (p.D608E) alteration is located in exon 18 (coding exon 18) of the DIXDC1 gene. This alteration results from a C to A substitution at nucleotide position 1824, causing the aspartic acid (D) at amino acid position 608 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
REVEL
Uncertain
Sift4G
Benign
T;T
Polyphen
D;.
Vest4
MutPred
Gain of phosphorylation at Y605 (P = 0.0968);.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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
No publications associated with this variant yet.