12-121856347-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002150.3(HPD):c.301G>A(p.Glu101Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,808 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002150.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HPD | NM_002150.3 | c.301G>A | p.Glu101Lys | missense_variant | Exon 6 of 14 | ENST00000289004.8 | NP_002141.2 | |
HPD | NM_001171993.2 | c.184G>A | p.Glu62Lys | missense_variant | Exon 8 of 16 | NP_001165464.1 | ||
TIALD | XR_002957437.2 | n.95C>T | non_coding_transcript_exon_variant | Exon 1 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HPD | ENST00000289004.8 | c.301G>A | p.Glu101Lys | missense_variant | Exon 6 of 14 | 1 | NM_002150.3 | ENSP00000289004.4 | ||
HPD | ENST00000543163.5 | c.184G>A | p.Glu62Lys | missense_variant | Exon 7 of 15 | 5 | ENSP00000441677.1 | |||
HPD | ENST00000542159.2 | n.337G>A | non_coding_transcript_exon_variant | Exon 3 of 6 | 5 | |||||
ENSG00000256811 | ENST00000543848.1 | n.89C>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461808Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727210
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.301G>A (p.E101K) alteration is located in exon 6 (coding exon 6) of the HPD gene. This alteration results from a G to A substitution at nucleotide position 301, causing the glutamic acid (E) at amino acid position 101 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