rs483352903
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_000354.6(SERPINA7):c.555del(p.Val186TrpfsTer3) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as association (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 23)
Consequence
SERPINA7
NM_000354.6 frameshift
NM_000354.6 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.35
Genes affected
SERPINA7 (HGNC:11583): (serpin family A member 7) There are three proteins including thyroxine-binding globulin (TBG), transthyretin and albumin responsible for carrying the thyroid hormones thyroxine (T4) and 3,5,3'-triiodothyronine (T3) in the bloodstream. This gene encodes the major thyroid hormone transport protein, TBG, in serum. It belongs to the serpin family in genomics, but the protein has no inhibitory function like many other members of the serpin family. Mutations in this gene result in TGB deficiency, which has been classified as partial deficiency, complete deficiency, and excess, based on the level of serum TBG. Alternatively spliced transcript variants encoding different isoforms have been found, but the full-length nature of these variants has not been determined.[provided by RefSeq, Jun 2012]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 10 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SERPINA7 | NM_000354.6 | c.555del | p.Val186TrpfsTer3 | frameshift_variant | 2/5 | ENST00000372563.2 | NP_000345.2 | |
SERPINA7 | XM_006724683.3 | c.555del | p.Val186TrpfsTer3 | frameshift_variant | 2/5 | XP_006724746.1 | ||
SERPINA7 | XM_005262180.5 | c.555del | p.Val186TrpfsTer3 | frameshift_variant | 2/5 | XP_005262237.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SERPINA7 | ENST00000372563.2 | c.555del | p.Val186TrpfsTer3 | frameshift_variant | 2/5 | 5 | NM_000354.6 | ENSP00000361644 | P1 | |
SERPINA7 | ENST00000327674.8 | c.555del | p.Val186TrpfsTer3 | frameshift_variant | 1/4 | 1 | ENSP00000329374 | P1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 genomes
Cov.:
23
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome Cov.: 23
GnomAD4 genome
Cov.:
23
ClinVar
Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Thyroxine-binding globulin quantitative trait locus Other:1
association, no assertion criteria provided | literature only | OMIM | Mar 01, 1992 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at