rs104894043
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PP3PP5BS2
The NM_000193.4(SHH):c.676G>A(p.Ala226Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000719 in 1,598,462 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A226G) has been classified as Uncertain significance.
Frequency
Consequence
NM_000193.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHH | NM_000193.4 | c.676G>A | p.Ala226Thr | missense_variant | 3/3 | ENST00000297261.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHH | ENST00000297261.7 | c.676G>A | p.Ala226Thr | missense_variant | 3/3 | 1 | NM_000193.4 | P1 | |
SHH | ENST00000430104.5 | c.301+2683G>A | intron_variant | 1 | |||||
SHH | ENST00000435425.1 | c.301+2683G>A | intron_variant, NMD_transcript_variant | 1 | |||||
SHH | ENST00000441114.5 | c.301+2683G>A | intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000437 AC: 10AN: 228672Hom.: 0 AF XY: 0.0000394 AC XY: 5AN XY: 126834
GnomAD4 exome AF: 0.0000740 AC: 107AN: 1446262Hom.: 0 Cov.: 35 AF XY: 0.0000708 AC XY: 51AN XY: 719972
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74358
ClinVar
Submissions by phenotype
Holoprosencephaly 3 Pathogenic:3
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 1997 | - - |
Pathogenic, no assertion criteria provided | curation | GeneReviews | Aug 29, 2013 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jul 19, 2023 | ClinVar contains an entry for this variant (Variation ID: 8883). This missense change has been observed in individuals with midline defects (PMID: 9302262, 22897141, 29205322). This variant is present in population databases (rs104894043, gnomAD 0.009%). This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 226 of the SHH protein (p.Ala226Thr). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SHH protein function. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Experimental studies have shown that this missense change affects SHH function (PMID: 15292211, 22897141). - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2019 | - - |
Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Laboratory of Human Genetics, Universidade de São Paulo | Jan 16, 2019 | Maternal inheritance. Presence of the variant confirmed by sanger in one sister and absent in the other. SHH pathogenic variants have incomplete penetrance and variable expressivity. Further, the phenotype is not suggestive of variants in this gene. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at