X-153725267-A-G

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1 PS1_Moderate PM2 PP5_Moderate

The NM_000033.4(ABCD1):c.1A>G(p.Met1?) variant causes a start lost 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 Pathogenic (★).

• Frequency: Genomes: not found (cov: 25)
• Consequence: ABCD1 NM_000033.4 start_lost
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 1.12

Genes affected

ABCD1 (HGNC:61): (ATP binding cassette subfamily D member 1) The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ALD subfamily, which is involved in peroxisomal import of fatty acids and/or fatty acyl-CoAs in the organelle. All known peroxisomal ABC transporters are half transporters which require a partner half transporter molecule to form a functional homodimeric or heterodimeric transporter. This peroxisomal membrane protein is likely involved in the peroxisomal transport or catabolism of very long chain fatty acids. Defects in this gene have been identified as the underlying cause of adrenoleukodystrophy, an X-chromosome recessively inherited demyelinating disorder of the nervous system. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PVS1: Start lost variant, no new inframe start found.
• PS1: Another start lost variant in NM_000033.4 (ABCD1) was described as [Pathogenic] in ClinVar as 2765282
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant X-153725267-A-G is Pathogenic according to our data. Variant chrX-153725267-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 851448.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-153725267-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCD1	NM_000033.4	c.1A>G	p.Met1?	start_lost	1/10	ENST00000218104.6
ABCD1	XM_047441916.1	c.1A>G	p.Met1?	start_lost	1/11
ABCD1	XM_047441917.1	c.1A>G	p.Met1?	start_lost	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCD1	ENST00000218104.6	c.1A>G	p.Met1?	start_lost	1/10	1	NM_000033.4	P1

Frequencies

GnomAD3 genomes Cov.: 25

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 25

Bravo AF: 0.00000756

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Adrenoleukodystrophy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Feb 05, 2019

This sequence change affects the initiator methionine of the ABCD1 mRNA. The next in-frame methionine is located at codon 67. For these reasons, this variant has been classified as Pathogenic. This variant has been reported to affect ABCD1 protein function (PMID: 22176151, 18206987). Disruption of the initiator codon has been observed in an individual affected with adrenoleukodystrophy (PMID: 22176151) and also segregated with adrenoleukodystrophy in a family (PMID: 18306728). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.55	D
BayesDel_noAF	Pathogenic	0.56
Cadd	Benign	21
Dann	Uncertain	0.99
DEOGEN2	Uncertain	0.49	T
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.90	D
M_CAP	Pathogenic	0.99	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Uncertain	0.24	D
MutationTaster	Benign	1.0	D
PROVEAN	Benign	-1.1	N
REVEL	Uncertain	0.59
Sift	Uncertain	0.021	D
Sift4G	Benign	0.071	T
Polyphen		0.028	B
Vest4		0.95
MutPred		0.99		Loss of MoRF binding (P = 0.1335);
MVP		1.0
ClinPred		0.95	D
GERP RS		5.1
Varity_R		0.52
gMVP		0.57

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: rs2091702389; hg19: chrX-152990722;