rs587784402

Variant names:

• chrX-135998860-A-G
• rs587784402
• NM_001379110.1:c.529A>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001379110.1(SLC9A6):​c.529A>G​(p.Ile177Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,075,236 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 0.0000019 (0 hom. 1 hem.)
• Consequence: SLC9A6 NM_001379110.1 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:2
• Conservation: PhyloP100: 0.530

Genes affected

SLC9A6 (HGNC:11079): (solute carrier family 9 member A6) This gene encodes a sodium-hydrogen exchanger that is amember of the solute carrier family 9. The encoded protein localizes to early and recycling endosomes and may be involved in regulating endosomal pH and volume. Defects in this gene are associated with X-linked syndromic cognitive disability, Christianson type. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Apr 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.11040133).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC9A6	NM_001379110.1	c.529A>G	p.Ile177Val	missense_variant	Exon 6 of 18	ENST00000630721.3	NP_001366039.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC9A6	ENST00000630721.3	c.529A>G	p.Ile177Val	missense_variant	Exon 6 of 18	4	NM_001379110.1	ENSP00000487486.2
SLC9A6	ENST00000370695.8	c.685A>G	p.Ile229Val	missense_variant	Exon 5 of 16	1		ENSP00000359729.4
SLC9A6	ENST00000370698.7	c.589A>G	p.Ile197Val	missense_variant	Exon 5 of 16	1		ENSP00000359732.3
SLC9A6	ENST00000370701.6	c.529A>G	p.Ile177Val	missense_variant	Exon 6 of 17	1		ENSP00000359735.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD3 exomes AF: 0.00000545 AC: 1 AN: 183385 Hom.: 0 AF XY: 0.0000147 AC XY: 1 AN XY: 67851

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: 0.0000122

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000186 AC: 2 AN: 1075236 Hom.: 0 Cov.: 27 AF XY: 0.00000291 AC XY: 1 AN XY: 343642

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: 0.00000244

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 23

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Uncertain:1

Jul 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

SLC9A6: PM2 -

Christianson syndrome Uncertain:1

Mar 18, 2014

Genetic Services Laboratory, University of Chicago

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.058
BayesDel_addAF	Benign	-0.45	T
BayesDel_noAF	Benign	-0.88
CADD	Benign	17
DANN	Uncertain	0.98
DEOGEN2	Benign	0.086	.;.;.;.;.;.;.;T;T;.
FATHMM_MKL	Benign	0.17	N
LIST_S2	Benign	0.83	.;.;T;.;.;T;T;T;T;T
M_CAP	Benign	0.0061	T
MetaRNN	Benign	0.11	T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.1	.;.;.;.;.;.;.;L;.;.
PrimateAI	Uncertain	0.53	T
PROVEAN	Benign	-0.53	.;.;.;.;.;N;N;N;.;.
REVEL	Benign	0.074
Sift	Benign	0.25	.;.;.;.;.;T;T;T;.;.
Sift4G	Benign	0.24	.;.;.;.;.;T;T;T;T;.
Polyphen		0.0, 0.0010	.;.;.;.;.;.;B;B;.;.
Vest4		0.13, 0.15, 0.12
MutPred		0.66		.;.;.;.;.;.;.;Loss of stability (P = 0.523);.;.;
MVP		0.15
MPC		0.88
ClinPred		0.085	T
GERP RS		4.3
Varity_R		0.16
gMVP		0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs587784402; hg19: chrX-135081019; COSMIC: COSV65789120;