X-55009249-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1 PM2 BP4 BP6

The NM_000032.5(ALAS2):c.1695G>C(p.Glu565Asp) 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 benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E565Q) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 23)
• Consequence: ALAS2 NM_000032.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:1
• Conservation: PhyloP100: 0.779

Genes affected

ALAS2 (HGNC:397): (5'-aminolevulinate synthase 2) The product of this gene specifies an erythroid-specific mitochondrially located enzyme. The encoded protein catalyzes the first step in the heme biosynthetic pathway. Defects in this gene cause X-linked pyridoxine-responsive sideroblastic anemia. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 3 uncertain in NM_000032.5
• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.26509172).
• BP6: Variant X-55009249-C-G is Benign according to our data. Variant chrX-55009249-C-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 2634710.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALAS2	NM_000032.5	c.1695G>C	p.Glu565Asp	missense_variant	11/11	ENST00000650242.1
ALAS2	NM_001037968.4	c.1656G>C	p.Glu552Asp	missense_variant	11/11
ALAS2	NM_001037967.4	c.1584G>C	p.Glu528Asp	missense_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALAS2	ENST00000650242.1	c.1695G>C	p.Glu565Asp	missense_variant	11/11		NM_000032.5	P1
ALAS2	ENST00000396198.7	c.1656G>C	p.Glu552Asp	missense_variant	11/11	5
ALAS2	ENST00000335854.8	c.1584G>C	p.Glu528Asp	missense_variant	10/10	2
ALAS2	ENST00000498636.1	c.824G>C	p.Ser275Thr	missense_variant	5/5	3

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD3 exomes AF: 0.00000585 AC: 1 AN: 170826 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 57204

Gnomad AFR exome AF: 0.0000815

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: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 23

Bravo AF: 0.00000378

ESP6500AA AF: 0.000261 AC: 1

ESP6500EA AF: 0.00 AC: 0

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

ALAS2-related disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Apr 20, 2023

The ALAS2 c.1695G>C variant is predicted to result in the amino acid substitution p.Glu565Asp. To our knowledge, this variant has not been reported in patients with ALAS2-related disorder. However, in a functional analysis, this variant was found to result in a small gain of function in enzymatic activity (Tchaikovskii et al. 2019. PubMed ID: 30678654). This variant is reported in 0.0081% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/X-55035682-C-G). Of note, a different variant impacting the same amino acid residue (p.Glu565Lys) has been reported in a patient with sideroblastic anemia onset in the third decade of life (Liu et al. 2013. PubMed ID: 24323989). At this time, the clinical significance of the c.1695G>C (p.Glu565Asp) variant is uncertain due to the absence of conclusive functional and genetic evidence. -

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

May 15, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.087
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.43
Cadd	Benign	17
Dann	Uncertain	0.99
FATHMM_MKL	Benign	0.64	D
LIST_S2	Benign	0.83	T;.;T;T
M_CAP	Pathogenic	0.60	D
MetaRNN	Benign	0.27	T;T;T;T
MetaSVM	Uncertain	-0.26	T
MutationTaster	Benign	0.92	D;D;D
PrimateAI	Benign	0.48	T
PROVEAN	Benign	-0.51	N;.;N;N
REVEL	Uncertain	0.32
Sift	Benign	0.32	T;.;T;T
Sift4G	Benign	0.38	T;.;T;T
Polyphen		0.0010	.;B;B;.
Vest4		0.12
MutPred		0.50		.;Gain of relative solvent accessibility (P = 0.0479);Gain of relative solvent accessibility (P = 0.0479);.;
MVP		0.72
MPC		0.45
ClinPred		0.24	T
GERP RS		2.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.28
gMVP		0.51

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: rs149747514; hg19: chrX-55035682;