rs104894950
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_004615.4(TSPAN7):c.652G>T(p.Gly218*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 23)
Consequence
TSPAN7
NM_004615.4 stop_gained
NM_004615.4 stop_gained
Scores
5
1
6
Clinical Significance
Conservation
PhyloP100: 9.25
Publications
2 publications found
Genes affected
TSPAN7 (HGNC:11854): (tetraspanin 7) The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein is a cell surface glycoprotein and may have a role in the control of neurite outgrowth. It is known to complex with integrins. This gene is associated with X-linked cognitive disability and neuropsychiatric diseases such as Huntington's chorea, fragile X syndrome and myotonic dystrophy. [provided by RefSeq, Jul 2008]
TSPAN7 Gene-Disease associations (from GenCC):
- intellectual disability, X-linked 58Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
- non-syndromic X-linked intellectual disabilityInheritance: XL Classification: MODERATE, SUPPORTIVE Submitted by: ClinGen, Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 11 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;
PP5
Variant X-38681258-G-T is Pathogenic according to our data. Variant chrX-38681258-G-T is described in ClinVar as Pathogenic. ClinVar VariationId is 11629.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| TSPAN7 | NM_004615.4 | c.652G>T | p.Gly218* | stop_gained | Exon 6 of 8 | ENST00000378482.7 | NP_004606.2 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
23
GnomAD4 exome Cov.: 29
GnomAD4 exome
Cov.:
29
GnomAD4 genome
GnomAD4 genome
Cov.:
23
Alfa
AF:
Hom.:
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Intellectual disability, X-linked 58 Pathogenic:1
Feb 01, 2000
OMIM
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:literature only
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
.;.;.
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
.;.;.
MetaRNN
Benign
.;.;.
MutationAssessor
Benign
.;.;.
PhyloP100
PROVEAN
Benign
.;.;.
REVEL
Benign
Sift
Pathogenic
.;.;.
Sift4G
Pathogenic
.;.;.
Vest4
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
Splicevardb
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DL_spliceai
Position offset: 29
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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