chrX-153694748-C-A

Variant names:

• chrX-153694748-C-A
• rs140601882
• NM_005629.4:c.1626C>A

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_005629.4(SLC6A8):​c.1626C>A​(p.Tyr542*) variant causes a stop gained change involving the alteration of a non-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 (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 25)
• Consequence: SLC6A8 NM_005629.4 stop_gained
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: -0.0440

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]

ACMG classification

Verdict is Pathogenic. Variant got 12 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-153694748-C-A is Pathogenic according to our data. Variant chrX-153694748-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 975971.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC6A8	NM_005629.4	c.1626C>A	p.Tyr542*	stop_gained	Exon 12 of 13	ENST00000253122.10	NP_005620.1
SLC6A8	NM_001142805.2	c.1596C>A	p.Tyr532*	stop_gained	Exon 12 of 13		NP_001136277.1
SLC6A8	NM_001142806.1	c.1281C>A	p.Tyr427*	stop_gained	Exon 12 of 13		NP_001136278.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC6A8	ENST00000253122.10	c.1626C>A	p.Tyr542*	stop_gained	Exon 12 of 13	1	NM_005629.4	ENSP00000253122.5
SLC6A8	ENST00000430077.6	c.1281C>A	p.Tyr427*	stop_gained	Exon 12 of 13	2		ENSP00000403041.2
SLC6A8	ENST00000485324.1	n.1933C>A		non_coding_transcript_exon_variant	Exon 5 of 6	2
SLC6A8	ENST00000413787.1	c.*172C>A		downstream_gene_variant		5		ENSP00000400463.1

Frequencies

GnomAD3 genomes Cov.: 25

GnomAD4 exome Cov.: 38

GnomAD4 genome Cov.: 25

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Creatine transporter deficiency Pathogenic:1

Jan 01, 2019

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was identified as de novo. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.74	D
BayesDel_noAF	Pathogenic	0.25
CADD	Benign	20
DANN	Benign	0.89
FATHMM_MKL	Uncertain	0.77	D
Vest4		0.79
GERP RS		-1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: rs140601882; hg19: chrX-152960203;