rs76723693

Variant names:

• chrX-154533025-A-G
• rs76723693
• NM_001360016.2:c.968T>C
• G6PD p.Leu323Pro

Variant summary

Our verdict is Pathogenic. The variant received 14 ACMG points: 16P and 2B. PS3 PM1 PP2 PP3 PP5_Very_Strong BP4 BS2_Supporting

The NM_001360016.2(G6PD):​c.968T>C​(p.Leu323Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000254 in 1,211,131 control chromosomes in the GnomAD database, including 1 homozygotes. There are 79 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). ClinVar reports functional evidence for this variant: "SCV000915298: Functional studies in E. coli demonstrated the p.Leu323Pro variant shows 50% residual activity compared to the wildtype enzyme and results in reduced substrate affinity and G6PD expression (Ramirez-Nava et al. 2017)." and additional evidence is available in ClinVar. Synonymous variant affecting the same amino acid position (i.e. L323L) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.0015 (1 hom., 46 hem., cov: 25)
  • Exomes 𝑓: 0.00013 (0 hom. 33 hem.)
• Consequence: G6PD NM_001360016.2 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:19 U:1
• Conservation: PhyloP100: 3.80
• Publications: 90 publications found

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 Gene-Disease associations (from GenCC):

• anemia, nonspherocytic hemolytic, due to G6PD deficiency

  Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae)
• G6PD deficiency

  Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
• class I glucose-6-phosphate dehydrogenase deficiency

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 14 ACMG points.

• PS3: PS3 evidence extracted from ClinVar submissions: SCV000915298: Functional studies in E. coli demonstrated the p.Leu323Pro variant shows 50% residual activity compared to the wildtype enzyme and results in reduced substrate affinity and G6PD expression (Ramirez-Nava et al. 2017).; SCV001142505: Functional studies demonstrated the p.Leu323Pro has a major contribution to the loss of affinity for both substrates in the double mutant G6PD A-. PMID29072585; SCV001873905: Functional studies demonstrate that p.(L323P) is associated with significantly decreased G6PD activity, stability, and catalytic efficiency; a further decrease in activity is seen when p.(L323P) is co-expressed with p.(N126D) (PMID: 29072585); SCV006325194: This particular variant has been reported in the heterozygous state and the hemizygous state in multiple individuals with G6PD deficiency (PMID: 22963789).; SCV001572468: Experimental evidence has reported a reduction in G6PD activity in cells expressing either [c.466A>G, c.1058T>C] or c.1058T>C in isolation. In the same study, c.1058T>C was also shown to significantly reduce affinity for substrates G6P and NADP+. (Ramirez-Nava_2017).; SCV002051813: "In vitro functional studies have shown a reduction in G6PD activity (less than 50% enzyme activity) in cells expressing either c.[376A>G;968T>C] or c.968T>C in isolation."; SCV002599252: activity was decreased in red blood cells of hemizygote (51%) (PS3).; SCV001572525: At least one publication reports experimental evidence indicating reduced G6PD activity and substrate affinity in cells expressing the complex variant (e.g. Ramirez-Nava_2017).; SCV002599350: Decreased activity in red blood cells (2-25%) and when expressed in E. coli (PS3).
• PM1: In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 5 uncertain in NM_001360016.2
• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 185 curated pathogenic missense variants (we use a threshold of 10). The gene has 42 curated benign missense variants. Gene score misZ: 2.0008 (below the threshold of 3.09). Trascript score misZ: NaN (below the threshold of 3.09). GenCC associations: The gene is linked to class I glucose-6-phosphate dehydrogenase deficiency, G6PD deficiency, anemia, nonspherocytic hemolytic, due to G6PD deficiency.
• PP3: Multiple lines of computational evidence support a deleterious effect 8: AlphaMissense, BayesDel_addAF, BayesDel_noAF, M_CAP, MutationAssessor, PROVEAN, REVEL, REVEL [when max_spliceai, FATHMM_MKL, MetaRNN, MutationTaster was below the threshold]
• PP5: Variant X-154533025-A-G is Pathogenic according to our data. Variant chrX-154533025-A-G is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 10388.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP4: Computational evidence support a benign effect (MetaRNN=0.01999113). . Strength limited to SUPPORTING due to the PP5.
• BS2: High Hemizygotes in GnomAd4 at 46 XL geneVariant has number of hemizygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001360016.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	G6PD	NM_001360016.2	MANE Select	c.968T>C	p.Leu323Pro	missense	Exon 9 of 13	NP_001346945.1	A0A384NL00
	G6PD	NM_000402.4		c.1058T>C	p.Leu353Pro	missense	Exon 9 of 13	NP_000393.4	P11413-3
	G6PD	NM_001042351.3		c.968T>C	p.Leu323Pro	missense	Exon 9 of 13	NP_001035810.1	P11413-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	G6PD	ENST00000393562.10	TSL:1 MANE Select	c.968T>C	p.Leu323Pro	missense	Exon 9 of 13	ENSP00000377192.3	P11413-1
	G6PD	ENST00000696421.1		c.968T>C	p.Leu323Pro	missense	Exon 9 of 13	ENSP00000512616.1	A0A8Q3SIS5
	G6PD	ENST00000369620.6	TSL:5	c.1106T>C	p.Leu369Pro	missense	Exon 9 of 13	ENSP00000358633.2	P11413-2

Frequencies

GnomAD3 genomes AF: 0.00150 AC: 170 AN: 112973 Hom.: 1 Cov.: 25

Gnomad AFR AF: 0.00456

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00212

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00329

GnomAD2 exomes AF: 0.000530 AC: 97 AN: 183074 AF XY: 0.000355

Gnomad AFR exome AF: 0.00563

Gnomad AMR exome AF: 0.000766

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.000442

GnomAD4 exome AF: 0.000126 AC: 138 AN: 1098104 Hom.: 0 Cov.: 33 AF XY: 0.0000908 AC XY: 33 AN XY: 363514

African (AFR) AF: 0.00265 AC: 70 AN: 26401

American (AMR) AF: 0.000966 AC: 34 AN: 35205

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19384

East Asian (EAS) AF: 0.00 AC: 0 AN: 30206

South Asian (SAS) AF: 0.00 AC: 0 AN: 54147

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40418

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4137

European-Non Finnish (NFE) AF: 0.00000119 AC: 1 AN: 842111

Other (OTH) AF: 0.000716 AC: 33 AN: 46095

GnomAD4 genome AF: 0.00150 AC: 170 AN: 113027 Hom.: 1 Cov.: 25 AF XY: 0.00131 AC XY: 46 AN XY: 35183

African (AFR) AF: 0.00455 AC: 142 AN: 31208

American (AMR) AF: 0.00212 AC: 23 AN: 10845

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2652

East Asian (EAS) AF: 0.00 AC: 0 AN: 3559

South Asian (SAS) AF: 0.00 AC: 0 AN: 2752

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6351

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 219

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 53220

Other (OTH) AF: 0.00325 AC: 5 AN: 1540

Alfa AF: 0.000333 Hom.: 8

Bravo AF: 0.00175

ClinVar

ClinVar submissions

Significance: Pathogenic/Likely pathogenic

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
7	1	-	Anemia, nonspherocytic hemolytic, due to G6PD deficiency (8)
6	-	-	not provided (6)
3	-	-	G6PD deficiency (3)
1	-	-	G6PD-related disorder (1)
1	-	-	Malaria, susceptibility to (1)
1	-	-	Malaria, susceptibility to;C2720289:Anemia, nonspherocytic hemolytic, due to G6PD deficiency (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.64
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Pathogenic	0.67
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.98	D
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.84	T
M_CAP	Pathogenic	0.91	D
MetaRNN	Benign	0.020	T
MetaSVM	Pathogenic	0.84	D
MutationAssessor	Pathogenic	3.1	M
PhyloP100		3.8
PrimateAI	Uncertain	0.62	T
PROVEAN	Pathogenic	-4.6	D
REVEL	Pathogenic	0.81
Sift	Benign	0.048	D
Sift4G	Benign	0.068	T
Varity_R		0.97
gMVP		0.99
Mutation Taster		=21/79	disease causing (ClinVar)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs76723693;

hg19: chrX-153761240;