chr13-33109903-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_178006.4(STARD13):c.3017C>T(p.Pro1006Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 1,614,124 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1006H) has been classified as Uncertain significance.
Frequency
Consequence
NM_178006.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STARD13 | NM_178006.4 | c.3017C>T | p.Pro1006Leu | missense_variant | 12/14 | ENST00000336934.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STARD13 | ENST00000336934.10 | c.3017C>T | p.Pro1006Leu | missense_variant | 12/14 | 1 | NM_178006.4 | P4 | |
STARD13 | ENST00000255486.8 | c.2993C>T | p.Pro998Leu | missense_variant | 12/14 | 1 | A2 | ||
STARD13 | ENST00000567873.2 | c.2972C>T | p.Pro991Leu | missense_variant | 12/14 | 1 | A2 | ||
STARD13 | ENST00000399365.7 | c.2663C>T | p.Pro888Leu | missense_variant | 12/14 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251450Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135900
GnomAD4 exome AF: 0.000118 AC: 173AN: 1461892Hom.: 0 Cov.: 32 AF XY: 0.000114 AC XY: 83AN XY: 727246
GnomAD4 genome AF: 0.000105 AC: 16AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.3017C>T (p.P1006L) alteration is located in exon 12 (coding exon 12) of the STARD13 gene. This alteration results from a C to T substitution at nucleotide position 3017, causing the proline (P) at amino acid position 1006 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at