rs104895219
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1PM2PP3_StrongPP5_Very_Strong
The NM_001065.4(TNFRSF1A):c.236C>T(p.Thr79Met) variant causes a missense change. The variant allele was found at a frequency of 0.000000692 in 1,444,640 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 Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T79K) has been classified as Uncertain significance.
Frequency
Consequence
NM_001065.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFRSF1A | NM_001065.4 | c.236C>T | p.Thr79Met | missense_variant | 3/10 | ENST00000162749.7 | |
TNFRSF1A | NM_001346091.2 | c.-89C>T | 5_prime_UTR_variant | 2/9 | |||
TNFRSF1A | NM_001346092.2 | c.-342C>T | 5_prime_UTR_variant | 3/11 | |||
TNFRSF1A | NR_144351.2 | n.498C>T | non_coding_transcript_exon_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFRSF1A | ENST00000162749.7 | c.236C>T | p.Thr79Met | missense_variant | 3/10 | 1 | NM_001065.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.92e-7 AC: 1AN: 1444640Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 717094
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
TNF receptor-associated periodic fever syndrome (TRAPS) Pathogenic:5Other:1
Pathogenic, criteria provided, single submitter | clinical testing | Genetics and Molecular Pathology, SA Pathology | Jan 14, 2022 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India | Dec 23, 2021 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 02, 1999 | - - |
not provided, no classification provided | literature only | Unité médicale des maladies autoinflammatoires, CHRU Montpellier | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Nov 04, 2023 | This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 79 of the TNFRSF1A protein (p.Thr79Met). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with TNF receptor-associated periodic fever syndrome (PMID: 10199409, 13130484, 23965844, 24393624, 25936627). It has also been observed to segregate with disease in related individuals. This variant is also known as T50M. ClinVar contains an entry for this variant (Variation ID: 12336). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on TNFRSF1A protein function. Experimental studies have shown that this missense change affects TNFRSF1A function (PMID: 15312137, 20457915). For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital | Oct 04, 2020 | - - |
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jan 03, 2023 | Published functional studies demonstrate a damaging effect due to cytoplasmic retention, reduced protein surface expression, impaired binding of TNF-alpha, and activation of the TNF-R1 and inflammasome pathways (Todd et al., 2004; Greco et al., 2015).; 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; Also known as p.(T50M); This variant is associated with the following publications: (PMID: 24950168, 25888769, 24393624, 26598380, 21153350, 16684962, 15312137, 21282379, 23894535, 20457915, 10199409, 25936627, 27332769, 33440462, 11722598, 31586650, 33284430, 31562507, 35577052, 15570662, 23965844) - |
Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at