rs80338740

Positions:

• chrX-153693978-GTTC-G

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2 PM4_Supporting PP5_Very_Strong

The NM_005629.4(SLC6A8):​c.1222_1224delTTC​(p.Phe408del) variant causes a conservative inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000893 in 112,006 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency:
  • Genomes: 𝑓 0.0000089 (0 hom., 0 hem., cov: 24)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: SLC6A8 NM_005629.4 conservative_inframe_deletion
• Clinical Significance: Pathogenic reviewed by expert panel P:7 O:3
• Conservation: PhyloP100: 7.91

Genes affected

SLC6A8 (HGNC:11055): (solute carrier family 6 member 8) The protein encoded by this gene is a plasma membrane protein whose function is to transport creatine into and out of cells. Defects in this gene can result in X-linked creatine deficiency syndrome. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

SLC6A8 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 11 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_005629.4. Strenght limited to Supporting due to length of the change: 1aa.
• PP5: Variant X-153693978-GTTC-G is Pathogenic according to our data. Variant chrX-153693978-GTTC-G is described in ClinVar as [Pathogenic]. Clinvar id is 11698.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chrX-153693978-GTTC-G is described in Lovd as [Pathogenic]. Variant chrX-153693978-GTTC-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC6A8	NM_005629.4	c.1222_1224delTTC	p.Phe408del	conservative_inframe_deletion	8/13	ENST00000253122.10	NP_005620.1
SLC6A8	NM_001142805.2	c.1192_1194delTTC	p.Phe398del	conservative_inframe_deletion	8/13		NP_001136277.1
SLC6A8	NM_001142806.1	c.877_879delTTC	p.Phe293del	conservative_inframe_deletion	8/13		NP_001136278.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC6A8	ENST00000253122.10	c.1222_1224delTTC	p.Phe408del	conservative_inframe_deletion	8/13	1	NM_005629.4	ENSP00000253122.5

Frequencies

GnomAD3 genomes AF: 0.00000893 AC: 1 AN: 112006 Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0 AN XY: 34184

Gnomad AFR AF: 0.00

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: 0.0000188

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1066528 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 346804

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000893 AC: 1 AN: 112006 Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0 AN XY: 34184

Gnomad4 AFR AF: 0.00

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: 0.0000188

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000660 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7 Other:3

Revision: reviewed by expert panel

Submissions by phenotype

Creatine transporter deficiency Pathogenic:5 Other:3

Pathogenic, no assertion criteria provided	literature only	OMIM	Aug 01, 2002	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Oct 18, 2023	The p.Phe408del variant in SLC6A8 has been reported in the hemizygous state in at least 9 males with creatine transporter deficiency, including one de novo occurrence (Bizzi 2002 PMID: 12210795, Poo-Arguelles 2006 PMID: 16601898, Fons 2009 PMID: 19706062, Alcaide 2011 PMID: 21140503, Valayannopoulos 2012 PMID: 21660517, van de Kamp 2013 PMID: 23644449, Comeaux 2013 PMID: 23660394, Valayannopoulos 2013 PMID: 22644605). It has also been identified in 0.002% (1/53102) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant causes an in-frame deletion of the phenylalanine residue at position 408. In vitro functional studies support that this variant results in decreased creatine uptake (Poo-Arguelles 2006 PMID: 16601898, Fons 2009 PMID: 19706062). Furthermore, this variant was classified as Pathogenic on August 22, 2023 by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (Variation ID 11698). In summary, this variant meets criteria to be classified as pathogenic for X-linked creatine transporter deficiency. ACMG/AMP Criteria applied: PS4, PM6, PM2_Supporting, PM4_Supporting, PS3_Supporting, PP4. -
Pathogenic, reviewed by expert panel	curation	ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel, ClinGen	Aug 22, 2023	The NM_005629.4:c.1222_1224del variant in SLC6A8 is predicted to cause a change in the length of the protein (p.Phe408del)) due to an in-frame deletion of 1 amino acid in a non-repeat region (PM4). This variant is one of the most common variants in SLC6A8 identiified in individuals with Creatine transporter deficiency. It has been reported in at least 10 individuals with clinical symptoms consistent with creatine transporter deficiency and elevated urine creatine/creatinine ratio from various countires including Italy, Spain, China, India, and Turkey (PMIDs: 12210795, 16169544, 21140503, 22551696, 23644449, 23660394, 29396939, 33656256, 34974949) (PS4_Very Strong). One male patient had clinical features consistent with creatine transporter deficiency, marked reduction of brain creatine peak on MRS. elevated urine creatine/creatinine ratio, and undetectable creatine uptake in fibroblasts with 25 μmol/L creatine (PMID: 16601898) (PP4_Strong). In gnomAD v2.1.1, the highest population minor allele frequency is 0.00009370 (1/10672 alleles) in the European non-Finnish population which is lower than the ClinGen CCDS VCEP’s threshold for PM2_Supporting (<0.00002). This is the only allele reported in any population in gnomAD v2.1.1. and there are 0 homozygotes and 0 hemizygotes (PM2_Supporting). The variant was introduced into SLC6A8 cDNA by site-directed mutagenesis and expressed in Xenopus oocytes. Creatine transport was measured in the presence of 20uM creatine and was "severely impaired" (PMID: 22644605) (PS3_Supporting). Mutation Taster predicts that the variant is "disease-causing". In summary, this variant meets the criteria to be classified as pathogenic for creatine transporter deficiency. SLC6A8-specific ACMG/AMP criteria applied, as specified by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (Specifications Version 1.1.0): PM4, PS4_VeryStrong, PP4_Strong,, PP3, PS3_Supporting, PM2_Supporting. (Classification approved by the ClinGen CCDS VCEP, August 22, 2023) -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 20, 2023	Variant summary: SLC6A8 c.1222_1224delTTC (p.Phe408del) results in an in-frame deletion that is predicted to remove 1 amino acid from the encoded protein. The variant was absent in 133527 control chromosomes (gnomAD). c.1222_1224delTTC has been reported in the literature in multiple individuals affected with Creatine Deficiency, X-Linked (Alcaide_2011, van der Kamp_2013, Valayannopoulos_2013). 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, finding that the variant causes a loss of electrogenic and creatine transport activities in X. laevis oocytes (Valayannopoulos_2013). The following publications have been ascertained in the context of this evaluation (PMID: 23644449, 21140503, 22644605). Four submitters, including a ClinGen expert panel, 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	phenotyping only	GenomeConnect-Association for Creatine Deficiencies, Association for Creatine Deficiencies	-	Variant interpreted as Pathogenic and reported on 01-00-1900 by GTR ID 26957. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect facilitates ClinVar submission from the Association for Creatine Deficiencies registry and does not attempt to reinterpret the variant. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 16, 2023	This variant, c.1222_1224del, results in the deletion of 1 amino acid(s) of the SLC6A8 protein (p.Phe408del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs80338740, gnomAD 0.01%). This variant has been observed in individual(s) with laboratory findings that are highly specific for X-linked creatine deficiency syndrome (PMID: 12210795, 16601898, 19706062, 21140503, 23644449, 23660394). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 11698). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects SLC6A8 function (PMID: 22644605). For these reasons, this variant has been classified as Pathogenic. -
not provided, no classification provided	phenotyping only	GenomeConnect - Brain Gene Registry	-	Variant interpreted as Pathogenic and reported on 03-06-2023 by Lab GeneDx. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Dec 01, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 05, 2023	Published functional studies indicate the variant impairs creatine uptake and did not generate any current in the presence of creatine, indicating that the electrogenic property and/or transport property was lost (Valayannopoulos et al., 2013); In silico analysis supports a deleterious effect on protein structure/function; In-frame deletion of 1 amino acid in a non-repeat region predicted to critically alter the protein; This variant is associated with the following publications: (PMID: 15154114, 34050321, 21140503, 24962355, 12210795, 12536364, 17825809, 27408820, 16601898, 23644449, 22551696, 19955008, 29396939, 28191890, 34426522, 33656256, 33726816, 31440721, 34974949, 22644605) -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs80338740; hg19: chrX-152959433;