X-154532765-G-T

Position:

• chrX-154532765-G-T

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2 PP3_Moderate PP5_Very_Strong

The NM_001360016.2(G6PD):​c.1089C>A​(p.Asn363Lys) variant causes a missense 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 Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 25)
• Consequence: G6PD NM_001360016.2 missense
• Clinical Significance: Likely pathogenic criteria provided, multiple submitters, no conflicts P:3 O:1
• Conservation: PhyloP100: -1.21

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]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.877
• PP5: Variant X-154532765-G-T is Pathogenic according to our data. Variant chrX-154532765-G-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 10390.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154532765-G-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
G6PD	NM_001360016.2	c.1089C>A	p.Asn363Lys	missense_variant	10/13	ENST00000393562.10	NP_001346945.1
G6PD	NM_000402.4	c.1179C>A	p.Asn393Lys	missense_variant	10/13		NP_000393.4
G6PD	NM_001042351.3	c.1089C>A	p.Asn363Lys	missense_variant	10/13		NP_001035810.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
G6PD	ENST00000393562.10	c.1089C>A	p.Asn363Lys	missense_variant	10/13	1	NM_001360016.2	ENSP00000377192.3

Frequencies

GnomAD3 genomes Cov.: 25

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 25

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:3 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Anemia, nonspherocytic hemolytic, due to G6PD deficiency Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Aug 09, 2021	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Dec 01, 1990	- -
Likely pathogenic, criteria provided, single submitter	curation	Dunham Lab, University of Washington	Aug 12, 2022	Variant found in hemizygote with G6PD deficiency and CNSHA (PP4). Decreased activity in red blood cells (1%) (PS3). Not found in gnomAD (PM2). Post_P 0.949 (odds of pathogenicity 168.4, Prior_P 0.1). -

G6PD LOMA LINDA Other:1

other, no assertion criteria provided

literature only

OMIM

Dec 01, 1990

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.91
BayesDel_addAF	Uncertain	0.12	D
BayesDel_noAF	Uncertain	-0.070
CADD	Benign	0.36
DANN	Benign	0.97
DEOGEN2	Pathogenic	0.97	D;D;D;.
FATHMM_MKL	Benign	0.25	N
LIST_S2	Pathogenic	0.98	.;.;D;D
M_CAP	Pathogenic	0.33	D
MetaRNN	Pathogenic	0.88	D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Benign	1.9	M;M;M;.
PrimateAI	Pathogenic	0.84	D
PROVEAN	Pathogenic	-5.3	.;.;D;D
REVEL	Pathogenic	0.65
Sift	Uncertain	0.0070	.;.;D;D
Sift4G	Uncertain	0.011	D;.;D;T
Polyphen		1.0	D;D;D;.
Vest4		0.81
MutPred		0.76		Gain of MoRF binding (P = 0.0364);Gain of MoRF binding (P = 0.0364);Gain of MoRF binding (P = 0.0364);.;
MVP		0.96
MPC		2.2
ClinPred		1.0	D
GERP RS		-6.7
Varity_R		0.93
gMVP		0.96

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: rs137852329; hg19: chrX-153760980;