2-231072309-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002807.4(PSMD1):c.775C>A(p.Gln259Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,724 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002807.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PSMD1 | NM_002807.4 | c.775C>A | p.Gln259Lys | missense_variant | Exon 7 of 25 | ENST00000308696.11 | NP_002798.2 | |
PSMD1 | NM_001191037.2 | c.775C>A | p.Gln259Lys | missense_variant | Exon 7 of 24 | NP_001177966.1 | ||
PSMD1 | XM_017004517.3 | c.775C>A | p.Gln259Lys | missense_variant | Exon 7 of 18 | XP_016860006.1 | ||
PSMD1 | NR_034059.2 | n.764C>A | non_coding_transcript_exon_variant | Exon 6 of 24 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461724Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727160
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.775C>A (p.Q259K) alteration is located in exon 7 (coding exon 7) of the PSMD1 gene. This alteration results from a C to A substitution at nucleotide position 775, causing the glutamine (Q) at amino acid position 259 to be replaced by a lysine (K). 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
Publications
No publications associated with this variant yet.