12-53321423-G-T

Variant summary

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

The NM_015665.6(AAAS):c.43C>A(p.Gln15Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00016 in 1,614,112 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.00012 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00016 (0 hom.)
• Consequence: AAAS NM_015665.6 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:10 U:1
• Conservation: PhyloP100: 2.63

Genes affected

AAAS (HGNC:13666): (aladin WD repeat nucleoporin) The protein encoded by this gene is a member of the WD-repeat family of regulatory proteins and may be involved in normal development of the peripheral and central nervous system. The encoded protein is part of the nuclear pore complex and is anchored there by NDC1. Defects in this gene are a cause of achalasia-addisonianism-alacrima syndrome (AAAS), also called triple-A syndrome or Allgrove syndrome. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 12-53321423-G-T is Pathogenic according to our data. Variant chr12-53321423-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 5044.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-53321423-G-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AAAS	NM_015665.6	c.43C>A	p.Gln15Lys	missense_variant	1/16	ENST00000209873.9
AAAS	NM_001173466.2	c.43C>A	p.Gln15Lys	missense_variant	1/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AAAS	ENST00000209873.9	c.43C>A	p.Gln15Lys	missense_variant	1/16	1	NM_015665.6	P1

Frequencies

GnomAD3 genomes AF: 0.000125 AC: 19 AN: 152256 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000250

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000183 AC: 46 AN: 251366 Hom.: 0 AF XY: 0.000213 AC XY: 29 AN XY: 135888

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000867

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000555

Gnomad FIN exome AF: 0.0000462

Gnomad NFE exome AF: 0.000220

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000163 AC: 239 AN: 1461856 Hom.: 0 Cov.: 31 AF XY: 0.000173 AC XY: 126 AN XY: 727220

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.0000671

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000533

Gnomad4 FIN exome AF: 0.0000375

Gnomad4 NFE exome AF: 0.000163

Gnomad4 OTH exome AF: 0.0000828

GnomAD4 genome AF: 0.000125 AC: 19 AN: 152256 Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7 AN XY: 74390

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000250

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000705 Hom.: 0

Bravo AF: 0.000136

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000233 AC: 2

ExAC AF: 0.000231 AC: 28

EpiCase AF: 0.0000545

EpiControl AF: 0.000356

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:10 Uncertain:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Glucocorticoid deficiency with achalasia Pathogenic:6 Uncertain:1

Pathogenic, no assertion criteria provided	literature only	OMIM	Nov 01, 2001	- -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Aug 14, 2018	Across a selection of available literature, the AAAS c.43C>A (p.Gln15Lys) missense variant (also referred to as p.Gly14ValfsTer45) has been reported in a homozygous state in at least six individuals with achalasia-Addisonianism-alacrima syndrome (which is also referred to as triple A syndrome), and in a compound heterozygous state in at least three other affected families (Handschug et al. 2001; Sandrini et al. 2001; Houlden et al. 2002; Huebner et al. 2004; Strauss et al. 2008; Dumic et al, 2012). In at least two families who were compound heterozygous for this variant, parents were shown to be heterozygous carriers of the p.Gln15Lys variant. This variant was absent from at least 50 controls but is reported at a frequency of 0.000606 in the South Asian population from the Exome Aggregation Consortium. In fibroblasts from a patient heterozygous for the p.Gln15Lys variant, Krumbholz et al. (2006) observed two splice products after amplification from a forward primer in exon 1 and reverse primer in exon 2. They conclude that the c.43C>A variant creates a novel splice donor site resulting in a frameshift and premature truncation of the protein (referred to as p.Gly14ValfsTer45). Based on the collective evidence, the p.Gln15Lys variant is classified as pathogenic for achalasia-Addisonianism-alacrima syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	The missense variant p.Q15K in AAAS (NM_015665.6) (also referred to as p.Gly14ValfsTer45) has been reported both in homozygous as well as compound heterozygous state (Dumic et al,Huebner A et al,Sandrini F). Functional studies have shown that c.43 C>A activates a cryptic splice donor site (Krumbholz et al., 2006). It has been submitted to ClinVar as Pathogenic.The missense variant c.43C>A (p.Q15K) in AAAS (NM_015665.6) is observed in 17/30616 (0.0555%) alleles from individuals of South Asian background in the gnomAD dataset (Exome Aggregation Consortium et al., 2016), but was not seen in the homozygous state. In silico tools are bening in their predictions and the residue is conserved across species. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	Mar 15, 2019	The observed variant NM_015665.6:c.43C>A/p.Gln15Lys is a missense variation found in exon 1 of the AAAS gene. It is a known pathogenic variant (dbsnp: rs121918549) and has been reported in the ExAC and gnomAD database with an allele frequency of 0.0002317 and 0.0191, respectively. The in silico prediction of this variant is disease causing by MutationTaster2. Parents of this patients are heterozygote carriers of this mutation. In summary, this variant meets the ACMG criteria to be classified as pathogenic based upon the evidence stated above. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	May 23, 2022	Variant summary: AAAS c.43C>A (p.Gln15Lys) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. Several computational tools predict a significant impact on normal splicing: Four predict the variant strengthens a cryptic exonic 5' splice donor site located at nucleotide 41. At least one publication reports experimental evidence that this variant affects mRNA splicing due to the activation of the cryptic exonic splice donor site resulting in a frame shifted protein referred to as p.G14Vfs*45 (Krumbholz_2006). The variant allele was found at a frequency of 0.00018 in 251366 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in AAAS causing Glucocorticoid Deficiency With Achalasia (0.00018 vs 0.0011), allowing no conclusion about variant significance. c.43C>A has been reported in the literature as homozygous and compound heterozygous genotypes in multiple individuals affected with features of Glucocorticoid Deficiency With Achalasia (also referred to as AAA syndrome) (example, Handschug_2001, Houlden_2002, Dumic_2012, Krumbholz_2006). These data indicate that the variant is very likely to be associated with disease. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 (Pathogenic, n=5; VUS, n=1). Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Oct 19, 2022	- -
Uncertain significance, flagged submission	clinical testing	Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City	Sep 26, 2019	- -

not provided Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Oct 27, 2022	PP1, PP4, PM1, PM2, PM3_strong, PS3, PS4 -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 05, 2022	Published functional studies demonstrate activation of a cryptic splice donor site that results in a frameshift at codon Glycine 14, changes this to a Valine residue, and creates a premature Stop codon at position 45 of the new reading frame (Krumbholz et al., 2006); also reported as p.Gly14ValfsX45; Variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 11159947, 28655339, 15666842, 12730363, 22538409, 12429595, 18615337, 15217518, 11701718, 26622478, 18628786, 32185032, 31589614, 34426522, 32146693, 23073554, 16609705) -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 31, 2023	This sequence change replaces glutamine, which is neutral and polar, with lysine, which is basic and polar, at codon 15 of the AAAS protein (p.Gln15Lys). This variant is present in population databases (rs121918549, gnomAD 0.06%). This missense change has been observed in individual(s) with achalasia-addisonianism-alacrimia syndrome (PMID: 11159947, 22538409, 32146693). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 5044). 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 not expected to disrupt AAAS protein function with a negative predictive value of 80%. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.063	T
BayesDel_noAF	Uncertain	0.020
Cadd	Pathogenic	29
Dann	Benign	0.94
DEOGEN2	Benign	0.090	T;.;T
Eigen	Benign	0.13
Eigen_PC	Uncertain	0.22
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Benign	0.64	T;T;T
M_CAP	Benign	0.078	D
MetaRNN	Benign	0.13	T;T;T
MetaSVM	Benign	-0.36	T
MutationAssessor	Benign	0.81	L;L;.
MutationTaster	Benign	0.98	A;A;A
PrimateAI	Uncertain	0.53	T
PROVEAN	Benign	-0.83	N;N;N
REVEL	Uncertain	0.50
Sift	Benign	0.71	T;T;T
Sift4G	Benign	0.93	T;T;.
Polyphen		0.78	P;.;.
Vest4		0.73
MVP		0.84
MPC		0.085
ClinPred		0.16	T
GERP RS		4.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.47
gMVP		0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.92		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.92		Position offset: 3

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs121918549; hg19: chr12-53715207;