X-101412328-C-T
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2PP3PP5_Very_Strong
The NM_019597.5(HNRNPH2):c.340C>T(p.Arg114Trp) 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_019597.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HNRNPH2 | NM_019597.5 | c.340C>T | p.Arg114Trp | missense_variant | Exon 2 of 2 | ENST00000316594.6 | NP_062543.1 | |
HNRNPH2 | NM_001032393.3 | c.340C>T | p.Arg114Trp | missense_variant | Exon 2 of 2 | NP_001027565.1 | ||
RPL36A-HNRNPH2 | NM_001199973.2 | c.*336C>T | 3_prime_UTR_variant | Exon 5 of 5 | NP_001186902.2 | |||
RPL36A-HNRNPH2 | NM_001199974.2 | c.*336C>T | 3_prime_UTR_variant | Exon 4 of 4 | NP_001186903.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HNRNPH2 | ENST00000316594.6 | c.340C>T | p.Arg114Trp | missense_variant | Exon 2 of 2 | 1 | NM_019597.5 | ENSP00000361927.2 | ||
RPL36A-HNRNPH2 | ENST00000409170.3 | c.*336C>T | downstream_gene_variant | 4 | ENSP00000386655.4 | |||||
RPL36A-HNRNPH2 | ENST00000409338.5 | c.*336C>T | downstream_gene_variant | 4 | ENSP00000386974.2 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Intellectual disability, X-linked, syndromic, Bain type Pathogenic:2
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not provided Pathogenic:1
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31236915, 33728377, 34015165, 31943778, 32335897, 34907471, 37463454, 34490615, 33874999) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.