rs483352903

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

Scores

Not classified

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: 1.35
Variant links:
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
SERPINA7NM_000354.6 linkuse as main transcriptc.555del p.Val186TrpfsTer3 frameshift_variant 2/5 ENST00000372563.2 NP_000345.2
SERPINA7XM_006724683.3 linkuse as main transcriptc.555del p.Val186TrpfsTer3 frameshift_variant 2/5 XP_006724746.1
SERPINA7XM_005262180.5 linkuse as main transcriptc.555del p.Val186TrpfsTer3 frameshift_variant 2/5 XP_005262237.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SERPINA7ENST00000372563.2 linkuse as main transcriptc.555del p.Val186TrpfsTer3 frameshift_variant 2/55 NM_000354.6 ENSP00000361644 P1
SERPINA7ENST00000327674.8 linkuse as main transcriptc.555del p.Val186TrpfsTer3 frameshift_variant 1/41 ENSP00000329374 P1

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD4 exome
Cov.:
30
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 providedliterature onlyOMIMMar 01, 1992- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs483352903; hg19: chrX-105280494; API