Variant X-135994822-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate

The NM_001379110.1(SLC9A6):c.206A>G(p.His69Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000000911 in 1,098,073 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 23)

Exomes 𝑓: 9.1e-7 ( 0 hom. 0 hem. )

Consequence

SLC9A6
NM_001379110.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.65

Variant links:

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]

SLC9A6 links:

SLC9A6 (HGNC:):

SLC9A6 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP6

Variant X-135994822-A-G is Benign according to our data. Variant chrX-135994822-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 409978.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC9A6	NM_001379110.1 linkuse as main transcript	c.206A>G	p.His69Arg	missense_variant	3/18	ENST00000630721.3	NP_001366039.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SLC9A6	ENST00000630721.3 linkuse as main transcript	c.206A>G	p.His69Arg	missense_variant	3/18	4	NM_001379110.1	ENSP00000487486.2	A0A0D9SGH0
SLC9A6	ENST00000370695.8 linkuse as main transcript	c.362A>G	p.His121Arg	missense_variant	2/16	1		ENSP00000359729.4	Q92581-2
SLC9A6	ENST00000370698.7 linkuse as main transcript	c.362A>G	p.His121Arg	missense_variant	2/16	1		ENSP00000359732.3	Q92581-1
SLC9A6	ENST00000370701.6 linkuse as main transcript	c.206A>G	p.His69Arg	missense_variant	3/17	1		ENSP00000359735.1	Q92581-3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

9.11e-7

AC:

AN:

1098073

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

363437

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:

0.00000119

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Bravo

AF:

0.00000756

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Christianson syndrome

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 05, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.082

BayesDel_addAF

Uncertain

0.12

BayesDel_noAF

Uncertain

-0.070

CADD

Benign

DANN

Benign

0.84

DEOGEN2

Benign

0.17

.;.;.;.;.;.;.;T;T;.

FATHMM_MKL

Uncertain

0.96

LIST_S2

Uncertain

0.92

.;.;D;.;.;D;D;D;D;D

M_CAP

Benign

0.027

MetaRNN

Uncertain

0.43

T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.46

.;.;.;.;.;.;N;N;.;.

PrimateAI

Pathogenic

0.83

PROVEAN

Benign

-1.7

.;.;.;.;.;N;N;N;.;.

REVEL

Benign

0.27

Sift

Benign

0.68

.;.;.;.;.;T;T;T;.;.

Sift4G

Benign

0.61

.;.;.;.;.;T;T;T;T;.

Polyphen

0.0040, 0.0010

.;.;.;.;.;.;B;B;.;.

Vest4

0.43, 0.46, 0.49

MutPred

0.58

.;.;.;.;.;.;Gain of solvent accessibility (P = 0.0171);Gain of solvent accessibility (P = 0.0171);.;.;

MVP

0.93

MPC

1.7

ClinPred

0.53

GERP RS

5.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.51

gMVP

0.89

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

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