X-131274168-G-A

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_ModeratePM2PP5_Moderate

The NM_001555.5(IGSF1):​c.3790C>T​(p.Arg1264*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000273 in 1,097,790 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).

Frequency

Genomes: not found (cov: 23)
Exomes 𝑓: 0.0000027 ( 0 hom. 0 hem. )

Consequence

IGSF1
NM_001555.5 stop_gained

Scores

2
1
2

Clinical Significance

Pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 2.33
Variant links:
Genes affected
IGSF1 (HGNC:5948): (immunoglobulin superfamily member 1) This gene encodes a member of the immunoglobulin-like domain-containing superfamily. Proteins in this superfamily contain varying numbers of immunoglobulin-like domains and are thought to participate in the regulation of interactions between cells. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0551 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant X-131274168-G-A is Pathogenic according to our data. Variant chrX-131274168-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 1301901.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IGSF1NM_001555.5 linkc.3790C>T p.Arg1264* stop_gained Exon 19 of 20 ENST00000361420.8 NP_001546.2 Q8N6C5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IGSF1ENST00000361420.8 linkc.3790C>T p.Arg1264* stop_gained Exon 19 of 20 1 NM_001555.5 ENSP00000355010.3 Q8N6C5-1

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD3 exomes
AF:
0.00000547
AC:
1
AN:
182879
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
67463
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000123
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000273
AC:
3
AN:
1097790
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
363154
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000238
Gnomad4 OTH exome
AF:
0.0000217
GnomAD4 genome
Cov.:
23

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

X-linked central congenital hypothyroidism with late-onset testicular enlargement Pathogenic:1
Jul 07, 2020
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This nonsense variant found in exon 19 of 20 is predicted to result in loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay (NMD). This variant has been previously reported as a hemizygous change in a patient with Central Hypothyroidism (PMID: 31448769). It is present in the heterozygous state in the gnomAD population database at a frequency of 0.0005% (1/182879) and thus is presumed to be rare. Parental samples were not available for inheritance studies. Based on the available evidence, the c.3805C>T (p.Arg1269Ter) variant is classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.65
D
BayesDel_noAF
Pathogenic
0.57
CADD
Pathogenic
36
DANN
Uncertain
1.0
FATHMM_MKL
Benign
0.67
D
Vest4
0.82
GERP RS
3.6

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.17
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: rs1309588455; hg19: chrX-130408142; COSMIC: COSV63836218; COSMIC: COSV63836218; API