17-49973217-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_138281.3(DLX4):c.428C>T(p.Ala143Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000235 in 1,614,044 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138281.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DLX4 | NM_138281.3 | c.428C>T | p.Ala143Val | missense_variant | Exon 2 of 3 | ENST00000240306.5 | NP_612138.1 | |
DLX4 | NM_001934.4 | c.212C>T | p.Ala71Val | missense_variant | Exon 1 of 2 | NP_001925.2 | ||
DLX4 | XM_047435517.1 | c.212C>T | p.Ala71Val | missense_variant | Exon 2 of 3 | XP_047291473.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250270Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135544
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461822Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727218
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.428C>T (p.A143V) alteration is located in exon 2 (coding exon 2) of the DLX4 gene. This alteration results from a C to T substitution at nucleotide position 428, causing the alanine (A) at amino acid position 143 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
DLX4-related disorder Uncertain:1
The DLX4 c.428C>T variant is predicted to result in the amino acid substitution p.Ala143Val. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0018% of alleles in individuals of European (Non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at