NM_001374675.1:c.69G>T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_ModeratePP5_Moderate
The NM_001374675.1(HSF4):c.69G>T(p.Lys23Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_001374675.1 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSF4 | NM_001374675.1 | c.69G>T | p.Lys23Asn | missense_variant | Exon 1 of 13 | ENST00000521374.6 | NP_001361604.1 | |
HSF4 | NM_001040667.3 | c.69G>T | p.Lys23Asn | missense_variant | Exon 3 of 15 | NP_001035757.1 | ||
HSF4 | NM_001374674.1 | c.69G>T | p.Lys23Asn | missense_variant | Exon 1 of 13 | NP_001361603.1 | ||
HSF4 | NM_001538.4 | c.69G>T | p.Lys23Asn | missense_variant | Exon 3 of 15 | NP_001529.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HSF4 | ENST00000521374.6 | c.69G>T | p.Lys23Asn | missense_variant | Exon 1 of 13 | 1 | NM_001374675.1 | ENSP00000430947.2 | ||
ENSG00000265690 | ENST00000580114.5 | n.*598G>T | non_coding_transcript_exon_variant | Exon 3 of 5 | 5 | ENSP00000464271.1 | ||||
ENSG00000265690 | ENST00000580114.5 | n.*598G>T | 3_prime_UTR_variant | Exon 3 of 5 | 5 | ENSP00000464271.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1455628Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 724002
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Cataract 5 multiple types Pathogenic:1
This sequence change replaces lysine, which is basic and polar, with asparagine, which is neutral and polar, at codon 23 of the HSF4 protein (p.Lys23Asn). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with autosomal dominant congenital cataracts (PMID: 24637349). It has also been observed to segregate with disease in related individuals. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). For these reasons, this variant has been classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.