rs869025279
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP5BS2
The NM_138281.3(DLX4):c.546del(p.Gln183ArgfsTer57) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,551,798 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000016 ( 0 hom. )
Consequence
DLX4
NM_138281.3 frameshift
NM_138281.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.14
Genes affected
DLX4 (HGNC:2917): (distal-less homeobox 4) Many vertebrate homeo box-containing genes have been identified on the basis of their sequence similarity with Drosophila developmental genes. Members of the Dlx gene family contain a homeobox that is related to that of Distal-less (Dll), a gene expressed in the head and limbs of the developing fruit fly. The Distal-less (Dlx) family of genes comprises at least 6 different members, DLX1-DLX6. The DLX proteins are postulated to play a role in forebrain and craniofacial development. Three transcript variants have been described for this gene, however, the full length nature of one variant has not been described. Studies of the two splice variants revealed that one encoded isoform functions as a repressor of the beta-globin gene while the other isoform lacks that function. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PP5
Variant 17-49973760-TG-T is Pathogenic according to our data. Variant chr17-49973760-TG-T is described in ClinVar as [Pathogenic]. Clinvar id is 221288.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High AC in GnomAdExome4 at 23 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLX4 | NM_138281.3 | c.546del | p.Gln183ArgfsTer57 | frameshift_variant | 3/3 | ENST00000240306.5 | |
DLX4 | NM_001934.4 | c.330del | p.Gln111ArgfsTer57 | frameshift_variant | 2/2 | ||
DLX4 | XM_047435517.1 | c.330del | p.Gln111ArgfsTer57 | frameshift_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLX4 | ENST00000240306.5 | c.546del | p.Gln183ArgfsTer57 | frameshift_variant | 3/3 | 1 | NM_138281.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000343 AC: 7AN: 204174Hom.: 0 AF XY: 0.0000271 AC XY: 3AN XY: 110682
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GnomAD4 exome AF: 0.0000164 AC: 23AN: 1399566Hom.: 0 Cov.: 30 AF XY: 0.0000174 AC XY: 12AN XY: 691254
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74376
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Orofacial cleft 15 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 04, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at