rs587776600

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong

The NM_030777.4(SLC2A10):c.1334del(p.Gly445GlufsTer40) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000172 in 1,614,062 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.00012 ( 0 hom., cov: 33)

Exomes 𝑓: 0.00018 ( 0 hom. )

Consequence

SLC2A10
NM_030777.4 frameshift

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:10O:1

Conservation

PhyloP100: 9.48

Variant links:

Genes affected

SLC2A10 (HGNC:13444): (solute carrier family 2 member 10) This gene encodes a member of the class III facilitative glucose transporter family. The encoded protein plays a role in regulation of glucose homeostasis. Mutations in this gene have been associated with arterial tortuosity syndrome.[provided by RefSeq, Dec 2009]

SLC2A10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 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 20-46726907-AG-A is Pathogenic according to our data. Variant chr20-46726907-AG-A is described in ClinVar as [Pathogenic]. Clinvar id is 4587.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-46726907-AG-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A10	NM_030777.4 linkuse as main transcript	c.1334del	p.Gly445GlufsTer40	frameshift_variant	3/5	ENST00000359271.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A10	ENST00000359271.4 linkuse as main transcript	c.1334del	p.Gly445GlufsTer40	frameshift_variant	3/5	1	NM_030777.4	P1

Frequencies

GnomAD3 genomes

AF:

0.000118

AC:

AN:

152184

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000965

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000191

Gnomad OTH

AF:

0.000479

GnomAD3 exomes

AF:

0.0000835

AC:

AN:

251486

Hom.:

AF XY:

0.000103

AC XY:

AN XY:

135920

show subpopulations

Gnomad AFR exome

AF:

0.000123

Gnomad AMR exome

AF:

0.0000578

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:

0.000149

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000177

AC:

259

AN:

1461878

Hom.:

Cov.:

AF XY:

0.000172

AC XY:

125

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.0000896

Gnomad4 AMR exome

AF:

0.0000894

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:

0.000219

Gnomad4 OTH exome

AF:

0.000132

GnomAD4 genome

AF:

0.000118

AC:

AN:

152184

Hom.:

Cov.:

AF XY:

0.0000807

AC XY:

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.0000965

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000191

Gnomad4 OTH

AF:

0.000479

Alfa

AF:

0.0000712

Hom.:

Bravo

AF:

0.000106

EpiCase

AF:

0.000109

EpiControl

AF:

0.000119

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:10Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Arterial tortuosity syndrome

Pathogenic:7Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Nov 16, 2023	Variant summary: SLC2A10 c.1334delG (p.Gly445GlufsX40) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 8.4e-05 in 251486 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in SLC2A10 causing Arterial Tortuosity Syndrome (8.4e-05 vs 0.0016), allowing no conclusion about variant significance. c.1334delG has been reported in the literature in multiple homozygous individuals affected with Arterial Tortuosity Syndrome (e.g. Coucke_2006, Piccinelli_2021). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function (e.g. Coucke_2006). The most pronounced variant effect results in severely reduced mRNA and protein expression in homozygous patient cells compared to unaffected controls. The following publications have been ascertained in the context of this evaluation (PMID: 16550171, 34847858). Six submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jan 01, 2008	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jan 29, 2024	The p.Gly445GlufsX40 variant in SLC2A10 has been reported in the homozygous or compound heterozygous state in at least 8 individuals with arterial tortuosity syndrome (1 homozygote, 7 compound heterozygotes, the majority of whom had a second disease causing variant in SLC210A; Coucke 2006 PMID: 16550171, Callewaert 2008 PMID: 17935213, Ritelli 2009 PMID: 19781076, Hardin 2018 PMID: 28726533). This variant segregated with disease in 7 affected relatives from 3 families (Coucke 2006 PMID: 16550171, Callewaert 2008 PMID: 17935213). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 4587) and has been identified 0.019% (13/68030) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org, v3.1.2), which is consistent with a recessive carrier frequency. In vitro functional studies using of patient cells demonstrate a lack of protein in homozygous patients and about half of wild type expression in heterozygotes (Coucke 2006 PMID: 16550171), suggesting that this variant affects protein function. This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 445 and leads to a premature termination codon 40 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Biallelic loss of function of the SLC2A10 gene is an established disease mechanism in autosomal recessive arterial tortuosity syndrome. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive arterial tortuosity syndrome. ACMG/AMP Criteria applied: PVS1, PM3_VeryStrong, PP1_Strong, PS3_Supporting. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 16, 2023	This sequence change creates a premature translational stop signal (p.Gly445Glufs*40) in the SLC2A10 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC2A10 are known to be pathogenic (PMID: 17935213, 22488877, 23494979). This variant is present in population databases (rs758681965, gnomAD 0.01%). This premature translational stop signal has been observed in individuals with arterial tortuosity syndrome (PMID: 16550171, 17935213, 19781076, 28726533). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 4587). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Sep 01, 2021	The SLC2A10 c.1334delG; p.Gly445GlufsTer40 variant (rs587776600) is reported in the literature in the homozygous or compound heterozygous state in multiple individuals affected with arterial tortuosity syndrome, and segregates with disease in at least one family (Callewaert 2008, Coucke 2006, Hardin 2018, Ritelli 2009). This variant is reported in ClinVar (Variation ID: 4587), and is found in the non-Finnish European population with an allele frequency of 0.015% (20/129188 alleles) in the Genome Aggregation Database. This variant causes a frameshift by deleting a single nucleotide, so it is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. Functional analyses of patient cells demonstrate a lack of protein in homozygous patients and about half of wild type expression in heterozygotes (Coucke 2006). Based on available information, this variant is considered to be pathogenic. References: Callewaert BL et al. Arterial tortuosity syndrome: clinical and molecular findings in 12 newly identified families. Hum Mutat. 2008 Jan;29(1):150-8. Coucke PJ et al. Mutations in the facilitative glucose transporter GLUT10 alter angiogenesis and cause arterial tortuosity syndrome. Nat Genet. 2006 Apr;38(4):452-7. Hardin JS et al. Ophthalmic findings in patients with arterial tortuosity syndrome and carriers: A case series. Ophthalmic Genet. 2018 Jan-Feb;39(1):29-34. Ritelli M et al. Arterial tortuosity syndrome in two Italian paediatric patients. Orphanet J Rare Dis. 2009 Sep 25;4:20. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	May 08, 2020	- -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital	May 24, 2017	- -

Familial thoracic aortic aneurysm and aortic dissection

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 09, 2021

The c.1334delG pathogenic mutation, located in coding exon 3 of the SLC2A10 gene, results from a deletion of one nucleotide at nucleotide position 1334, causing a translational frameshift with a predicted alternate stop codon (p.G445Efs*40). This mutation was reported in association with arterial tortuosity syndrome (ATS) in the homozygous state in an Italian family with consanguinity (Coucke PJ et al. Nat Genet. 2006;38(4):452-7). This recurrent mutation, which is in the endofacial loop between TMD10 and TMD11, was also reported in four European families each in compound heterozygosity with another mutation (Callewaert BL et al. Hum Mutat. 2008;29(1):150-8). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -

not provided

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Feb 03, 2022

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Published functional studies demonstrate a damaging effect in SLC2A10-encoded protein levels in individuals homozygous for the variant that showed nearly absent expression, while heterozygous carriers in the family expressed about half the amount of protein compared to wild-type and deficiencies in protein transport (Coucke et al., 2006; Nemeth et al., 2016); Reported in ClinVar as a pathogenic variant (ClinVar Variant ID# 4587; ClinVar); This variant is associated with the following publications: (PMID: 27153185, 16550171, 17935213, 17163528, 19781076, 31589614, 28726533, 31786173) -

SLC2A10-related disorder

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Aug 02, 2023

The SLC2A10 c.1334delG variant is predicted to result in a frameshift and premature protein termination (p.Gly445Glufs*40). This variant has been reported in the homozygous and compound heterozygous state in multiple individuals with arterial tortuosity syndrome (Coucke et al. 2006. PubMed ID: 16550171; Callewaert et al. 2008. PubMed ID: 17935213; Hardin et al. 2018. PubMed ID: 28726533). This variant is reported in 0.015% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/20-45355546-AG-A). Frameshift variants in SLC2A10 are expected to be pathogenic. This variant is interpreted as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over