rs121909765
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1PM2PP3PP5_Very_Strong
The NM_001360.3(DHCR7):c.866C>T(p.Thr289Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,770 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 Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. T289T) has been classified as Likely benign.
Frequency
Consequence
NM_001360.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DHCR7 | NM_001360.3 | c.866C>T | p.Thr289Ile | missense_variant | 8/9 | ENST00000355527.8 | |
DHCR7 | NM_001163817.2 | c.866C>T | p.Thr289Ile | missense_variant | 8/9 | ||
DHCR7 | XM_011544777.3 | c.866C>T | p.Thr289Ile | missense_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DHCR7 | ENST00000355527.8 | c.866C>T | p.Thr289Ile | missense_variant | 8/9 | 1 | NM_001360.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251110Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135724
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461552Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727070
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
Smith-Lemli-Opitz syndrome Pathogenic:4
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 22, 2001 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 289 of the DHCR7 protein (p.Thr289Ile). This variant is present in population databases (rs121909765, gnomAD 0.004%). This missense change has been observed in individual(s) with Smith-Lemli-Opitz syndrome (PMID: 10995508, 11298379). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 6789). 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 expected to disrupt DHCR7 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | - | - - |
Likely pathogenic, no assertion criteria provided | clinical testing | Counsyl | Apr 06, 2016 | - - |
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Feb 22, 2022 | Not observed at a 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: 29300326, 11111101, 12914579, 16392899, 24500076, 11298379, 9714007, 10995508, 11186897, 11471166, 23603282, 12070263) - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Athena Diagnostics | Sep 21, 2020 | The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). This variant appears to segregate with disease in at least one family, however, the available information does not rule out segregation due to chance. Assessment of experimental evidence suggests this variant results in abnormal protein function. Elevated levels of 7-DHC were present in patients (PMID: 9714007). - |
Inborn genetic diseases Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | May 22, 2019 | The p.T289I pathogenic mutation (also known as c.866C>T), located in coding exon 6 of the DHCR7 gene, results from a C to T substitution at nucleotide position 866. The threonine at codon 289 is replaced by isoleucine, an amino acid with similar properties. This mutation has been reported in multiple individuals with Smith-Lemli-Opitz syndrome, in conjunction with a second disease-causing allele (Krakowiak PA et al. Am. J. Med. Genet., 2000 Sep;94:214-27; Nowaczyk MJ et al. Am. J. Med. Genet., 2001 Apr;100:162-3). Based on data from gnomAD, the T allele has an overall frequency of approximately 0.0016% (4/251110). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at