chr12-108535360-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_014706.4(SART3):āc.1555A>Gā(p.Arg519Gly) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,946 control chromosomes in the GnomAD database, with no homozygous occurrence. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Consequence
NM_014706.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SART3 | NM_014706.4 | c.1555A>G | p.Arg519Gly | missense_variant, splice_region_variant | 12/19 | ENST00000546815.6 | |
SART3 | NM_001410983.1 | c.1609A>G | p.Arg537Gly | missense_variant, splice_region_variant | 12/19 | ||
SART3 | XM_047429916.1 | c.691A>G | p.Arg231Gly | missense_variant, splice_region_variant | 7/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SART3 | ENST00000546815.6 | c.1555A>G | p.Arg519Gly | missense_variant, splice_region_variant | 12/19 | 5 | NM_014706.4 | P1 | |
ENST00000662962.1 | n.166-2156T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460946Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726824
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Intellectual disability, Neurodevelopmental defects and Developmental delay with 46,XY gonadal dysgenesis Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | Reproductive Development, Murdoch Childrens Research Institute | Mar 06, 2023 | This variant was identified in an affected child in trans with a second variant in SART3 c.2153C>T (compound heterozygous). This variant was inherited from a heterozgyous unaffected mother. It was identified as part of a larger study that has found biallelic variants in SART3 in nine children from six families with overlapping clinical features. The variant falls in a highly conserved residue within an important HAT protein domain. The variant is extremely rare or absent in population databases. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.