chrX-154546061-T-C

Position:

chrX-154546061-T-C

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM5PP5_Very_Strong

The NM_001360016.2(G6PD):c.95A>G(p.His32Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000306 in 1,209,146 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 10 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H32D) has been classified as Likely pathogenic.

Frequency

Genomes: 𝑓 0.000072 ( 0 hom., 5 hem., cov: 23)

Exomes 𝑓: 0.000026 ( 0 hom. 5 hem. )

Consequence

G6PD
NM_001360016.2 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 5.99

Variant links:

Genes affected

G6PD (HGNC:4057): (glucose-6-phosphate dehydrogenase) This gene encodes glucose-6-phosphate dehydrogenase. This protein is a cytosolic enzyme encoded by a housekeeping X-linked gene whose main function is to produce NADPH, a key electron donor in the defense against oxidizing agents and in reductive biosynthetic reactions. G6PD is remarkable for its genetic diversity. Many variants of G6PD, mostly produced from missense mutations, have been described with wide ranging levels of enzyme activity and associated clinical symptoms. G6PD deficiency may cause neonatal jaundice, acute hemolysis, or severe chronic non-spherocytic hemolytic anemia. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

G6PD links:

IKBKG (HGNC:5961): (inhibitor of nuclear factor kappa B kinase regulatory subunit gamma) This gene encodes the regulatory subunit of the inhibitor of kappaB kinase (IKK) complex, which activates NF-kappaB resulting in activation of genes involved in inflammation, immunity, cell survival, and other pathways. Mutations in this gene result in incontinentia pigmenti, hypohidrotic ectodermal dysplasia, and several other types of immunodeficiencies. A pseudogene highly similar to this locus is located in an adjacent region of the X chromosome. [provided by RefSeq, Mar 2016]

IKBKG links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 10 ACMG points.

PM5

Other missense variant is known to change same aminoacid residue: Variant chrX-154546062-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1722692.Status of the report is criteria_provided_single_submitter, 1 stars.

PP5

Variant X-154546061-T-C is Pathogenic according to our data. Variant chrX-154546061-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 10403.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154546061-T-C is described in Lovd as [Pathogenic]. Variant chrX-154546061-T-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
G6PD	NM_001360016.2 linkuse as main transcript	c.95A>G	p.His32Arg	missense_variant	2/13	ENST00000393562.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
G6PD	ENST00000393562.10 linkuse as main transcript	c.95A>G	p.His32Arg	missense_variant	2/13	1	NM_001360016.2	P4	P11413-1

Frequencies

GnomAD3 genomes

AF:

0.0000718

AC:

AN:

111476

Hom.:

Cov.:

AF XY:

0.000149

AC XY:

AN XY:

33668

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000952

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00196

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000148

AC:

AN:

182995

Hom.:

AF XY:

0.0000889

AC XY:

AN XY:

67465

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00195

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000264

AC:

AN:

1097670

Hom.:

Cov.:

AF XY:

0.0000138

AC XY:

AN XY:

363060

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000284

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000927

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:

0.0000718

AC:

AN:

111476

Hom.:

Cov.:

AF XY:

0.000149

AC XY:

AN XY:

33668

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.0000952

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00196

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000313

Hom.:

Bravo

AF:

0.0000907

ExAC

AF:

0.000132

AC:

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:10Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Anemia, nonspherocytic hemolytic, due to G6PD deficiency

Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 21, 2024	This sequence change replaces histidine, which is basic and polar, with arginine, which is basic and polar, at codon 32 of the G6PD protein (p.His32Arg). This variant is present in population databases (rs137852340, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with G6PD deficiency (PMID: 10502785, 11601226, 16329560, 29339739, 30315739). It is commonly reported in individuals of Asian ancestry (PMID: 29339739). This variant is also known as G6PD Gaohe. ClinVar contains an entry for this variant (Variation ID: 10403). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt G6PD protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Aug 09, 2023	- -
Pathogenic, criteria provided, single submitter	curation	Dunham Lab, University of Washington	Aug 12, 2022	Variant found in hemizygtes with G6PD deficiency, some with anemia and jaundice (PP4). Decreased activity in red blood cells of hemizygotes (0-38%) (PS3). Identified in unrelated individuals with G6PD deficiency (PS4_M). Modeling predicts disruption of function (PP3). Below expected carrier frequency in gnomAD (PM2). Post_P 0.994 (odds of pathogenicity 1517, Prior_P 0.1). -
Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 27, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Feb 02, 2022	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with G6PD deficient haemolytic anaemia (favism). (I) 0109 - This gene is associated with X-linked recessive disease. Hemizygous males and homozygous females are commonly affected, however some heterozygous female carriers can also be affected depending on X inactivation. (I) 0200 - Variant is predicted to result in a missense amino acid change from histidine to arginine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (22 heterozygotes, 0 homozygotes, 7 hemizygotes). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This founder mutation in Asian population that is also known as G6PD Gaohe have been reported in multiple individuals with G6PD deficiency (ClinVar, PMID: 29339739, 33051526). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Early-onset coronary artery disease

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Mar 08, 2024

- -

Inborn genetic diseases

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 12, 2022

The c.95A>G (p.H32R) alteration is located in exon 2 (coding exon 1) of the G6PD gene. This alteration results from an A to G substitution at nucleotide position 95, causing the histidine (H) at amino acid position 32 to be replaced by an arginine (R). Based on data from gnomAD, the G allele has an overall frequency of 0.014% (29/204635) total alleles studied. The highest observed frequency was 0.196% (29/14827) of East Asian alleles. This variant accounts for more than 20% of pathogenic alleles in the Chinese population and has been detected alone or in conjunction with another G6PD variant in individuals with G6PD deficiency (Chiu, 1993; Zhong, 2018; Chen, 2018; Fu, 2018; Ohlsson, 2019; He, 2020; Wang, 2021; Xu, 2021; Pan, 2021; Xu, 2022). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. -

Malaria, susceptibility to;C2720289:Anemia, nonspherocytic hemolytic, due to G6PD deficiency

Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

May 27, 2022

- -

Malaria, susceptibility to

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Mar 24, 2024

- -

G6PD deficiency

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Mar 08, 2024

Variant summary: G6PD c.185A>G (p.His62Arg) [NM_001035810.1:c.95A>G (p.His32Arg)], also referred to as G6PD Gaohe/Gaozhou/Sapporo-like/Ube/Bodia-like, results in a non-conservative amino acid change located in the Glucose-6-phosphate dehydrogenase, NAD-binding domain (IPR022674) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00015 in 182995 control chromosomes predominantly in the East Asian population. This frequency is not significantly higher than estimated for a pathogenic variant in G6PD causing Glucose 6 Phosphate Dehydrogenase Deficiency (0.00015 vs 0.29), allowing no conclusion about variant significance. c.185A>G has been reported in the literature in multiple individuals affected with Glucose 6 Phosphate Dehydrogenase Deficiency and as a G6PD hotspot mutation in the Chinese population (example, Ainoon_1999, Fu_2018, Sun_2022). At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal G6PD enzyme activity (Ainoon_1999). The following publications have been ascertained in the context of this evaluation (PMID: 10502785, 29339739, 16607506, 36353116). ClinVar contains an entry for this variant (Variation ID: 10403). Based on the evidence outlined above, the variant was classified as pathogenic. -

G6PD GAOHE

Other:1

other, no assertion criteria provided

literature only

OMIM

Sep 05, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.66

BayesDel_addAF

Pathogenic

0.32

BayesDel_noAF

Pathogenic

0.67

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Pathogenic

0.82

D;D;D;.;T;.;T

FATHMM_MKL

Uncertain

0.86

LIST_S2

Uncertain

0.92

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

M_CAP

Pathogenic

0.87

MetaRNN

Uncertain

0.64

D;D;D;D;D;D;D

MetaSVM

Pathogenic

0.97

MutationAssessor

Uncertain

2.1

M;M;M;M;.;.;.

MutationTaster

Benign

1.0

D;D;D;D;D;D

PrimateAI

Uncertain

0.74

PROVEAN

Uncertain

-4.3

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

REVEL

Pathogenic

0.78

Sift

Benign

0.27

.;.;T;T;T;T;D

Sift4G

Benign

0.34

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

Polyphen

1.0

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

Vest4

0.67

MutPred

0.85

Loss of disorder (P = 0.1672);Loss of disorder (P = 0.1672);Loss of disorder (P = 0.1672);Loss of disorder (P = 0.1672);Loss of disorder (P = 0.1672);Loss of disorder (P = 0.1672);Loss of disorder (P = 0.1672);

MVP

1.0

MPC

2.6

ClinPred

0.32

GERP RS

5.8

Varity_R

0.95

gMVP

0.97

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