chr3-51988821-C-T

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP5BP4BS1_SupportingBS2

The NM_000666.3(ACY1):c.1057C>T(p.Arg353Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0035 in 1,614,196 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0025 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0036 ( 15 hom. )

Consequence

ACY1
NM_000666.3 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:9U:8

Conservation

PhyloP100: 3.00

Variant links:

Genes affected

ACY1 (HGNC:177): (aminoacylase 1) This gene encodes a cytosolic, homodimeric, zinc-binding enzyme that catalyzes the hydrolysis of acylated L-amino acids to L-amino acids and an acyl group, and has been postulated to function in the catabolism and salvage of acylated amino acids. This gene is located on chromosome 3p21.1, a region reduced to homozygosity in small-cell lung cancer (SCLC), and its expression has been reported to be reduced or undetectable in SCLC cell lines and tumors. The amino acid sequence of human aminoacylase-1 is highly homologous to the porcine counterpart, and this enzyme is the first member of a new family of zinc-binding enzymes. Mutations in this gene cause aminoacylase-1 deficiency, a metabolic disorder characterized by central nervous system defects and increased urinary excretion of N-acetylated amino acids. Alternative splicing of this gene results in multiple transcript variants. Read-through transcription also exists between this gene and the upstream ABHD14A (abhydrolase domain containing 14A) gene, as represented in GeneID:100526760. A related pseudogene has been identified on chromosome 18. [provided by RefSeq, Nov 2010]

ACY1 links:

ABHD14A-ACY1 (HGNC:38856): (ABHD14A-ACY1 readthrough) This locus represents naturally occurring read-through transcription between the neighboring abhydrolase domain containing 14A (ABHD14A) and aminoacylase 1 (ACY1) genes on chromosome 3. The read-through transcript encodes a protein that shares sequence identity with the downstream gene product but its N-terminal region is distinct due to the use of an alternate start codon relative to the upstream gene. [provided by RefSeq, Oct 2015]

ABHD14A-ACY1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PP5

Variant 3-51988821-C-T is Pathogenic according to our data. Variant chr3-51988821-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 18110.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=8, Pathogenic=3, Likely_pathogenic=4}.

BP4

Computational evidence support a benign effect (MetaRNN=0.03669554). . Strength limited to SUPPORTING due to the PP5.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00253 (385/152318) while in subpopulation NFE AF= 0.00398 (271/68034). AF 95% confidence interval is 0.00359. There are 1 homozygotes in gnomad4. There are 193 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

BS2

High Homozygotes in GnomAdExome4 at 15 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACY1	NM_000666.3 link	c.1057C>T	p.Arg353Cys	missense_variant	Exon 14 of 15	ENST00000636358.2	NP_000657.1	Q03154-1V9HWA0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACY1	ENST00000636358.2 link	c.1057C>T	p.Arg353Cys	missense_variant	Exon 14 of 15	1	NM_000666.3	ENSP00000490149.1		Q03154-1
ABHD14A-ACY1	ENST00000463937.1 link	c.1360C>T	p.Arg454Cys	missense_variant	Exon 15 of 16	5		ENSP00000420487.1		C9JMV9

Frequencies

GnomAD3 genomes

AF:

0.00252

AC:

384

AN:

152200

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000748

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.000851

Gnomad ASJ

AF:

0.00230

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00292

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00398

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.00268

AC:

675

AN:

251440

Hom.:

AF XY:

0.00286

AC XY:

389

AN XY:

135884

show subpopulations

Gnomad AFR exome

AF:

0.000492

Gnomad AMR exome

AF:

0.00107

Gnomad ASJ exome

AF:

0.00258

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00203

Gnomad FIN exome

AF:

0.00323

Gnomad NFE exome

AF:

0.00404

Gnomad OTH exome

AF:

0.00163

GnomAD4 exome

AF:

0.00360

AC:

5266

AN:

1461878

Hom.:

Cov.:

AF XY:

0.00356

AC XY:

2592

AN XY:

727236

show subpopulations

Gnomad4 AFR exome

AF:

0.000508

Gnomad4 AMR exome

AF:

0.00119

Gnomad4 ASJ exome

AF:

0.00337

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00182

Gnomad4 FIN exome

AF:

0.00329

Gnomad4 NFE exome

AF:

0.00411

Gnomad4 OTH exome

AF:

0.00323

GnomAD4 genome

AF:

0.00253

AC:

385

AN:

152318

Hom.:

Cov.:

AF XY:

0.00259

AC XY:

193

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.000746

Gnomad4 AMR

AF:

0.000850

Gnomad4 ASJ

AF:

0.00230

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00124

Gnomad4 FIN

AF:

0.00292

Gnomad4 NFE

AF:

0.00398

Gnomad4 OTH

AF:

0.00520

Alfa

AF:

0.00374

Hom.:

Bravo

AF:

0.00263

TwinsUK

AF:

0.00270

AC:

ALSPAC

AF:

0.00545

AC:

ESP6500AA

AF:

0.000681

AC:

ESP6500EA

AF:

0.00349

AC:

ExAC

AF:

0.00261

AC:

317

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00458

EpiControl

AF:

0.00409

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:9Uncertain:8

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Aminoacylase 1 deficiency

Pathogenic:5Uncertain:4

Likely pathogenic, no assertion criteria provided	clinical testing	Medical Genetics Laboratory, Tarbiat Modares University	Mar 01, 2020	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jun 12, 2007	- -
Uncertain significance, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Jan 20, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Elsea Laboratory, Baylor College of Medicine	Apr 01, 2020	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genomic Research Center, Shahid Beheshti University of Medical Sciences	Dec 03, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	New York Genome Center	Jul 10, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Sep 04, 2024	Variant summary: ACY1 c.1057C>T (p.Arg353Cys) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0027 in 251440 control chromosomes, predominantly at a frequency of 0.004 within the Non-Finnish European subpopulation in the gnomAD database, including 2 homozygotes. Due to the extremely low prevalence of this condition, this frequency does not allow conclusions about variant significance. Furthermore, the clinical/biochemical phenotype, family history or follow-up on the two homozygous individuals reported in the gnomAD database is not known. c.1057C>T has been reported in the literature as homozygous and compound heterozygous genotypes in individuals affected with Aminoacylase I deficiency supported by characteristic biochemical organic acid profiles (Van Coster_2005, Tylki-Szymanska_2010, Sass_2016, Smolka_2023, Kunisetty_2024). The ages of presentation were variable ranging from newborn stage to childhood for homozygous cases reports (Van Coster_2005, Tylki-Szymanska_2010, Smolka_2023, Kunisetty_2024) to a 63 year old compound heterozygous woman with dystonic symptoms starting at age 12 (Sass_2016). These data indicate that the variant is very likely to be associated with disease. However, the possibility of ACY1 deficiency having a pathogenic significance with pleiotropic clinical expression versus simply a biochemical variant phenotype has been speculated (Sass_2006). At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <1% of normal Aminoacylase I enzyme activity in lymphoblasts from a homozygous individual (Van Coster_2005). The following publications have been ascertained in the context of this evaluation (PMID: 26686503, 21414403, 20480396, 16274666, 38502138, 38234346). ClinVar contains an entry for this variant (Variation ID: 18110). Based on the evidence outlined above, the variant was classified as likely pathogenic. -
Uncertain significance, criteria provided, single submitter	clinical testing	Daryl Scott Lab, Baylor College of Medicine	Nov 10, 2023	- -

not provided

Pathogenic:2Uncertain:4

Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Mar 09, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 07, 2022	This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 353 of the ACY1 protein (p.Arg353Cys). This variant is present in population databases (rs121912698, gnomAD 0.4%), including at least one homozygous and/or hemizygous individual. This missense change has been observed in individual(s) with aminoacylase 1 deficiency (PMID: 16274666, 16465618, 17562838, 20480396, 26686503). ClinVar contains an entry for this variant (Variation ID: 18110). 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 expected to disrupt ACY1 protein function. Experimental studies have shown that this missense change affects ACY1 function (PMID: 21414403, 26686503). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Sep 29, 2015	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Sep 06, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Feb 01, 2025	ACY1: PM3:Very Strong, PM2:Supporting, PS3:Supporting -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -

Inborn genetic diseases

Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 02, 2022

The c.1057C>T (p.R353C) alteration is located in exon 14 (coding exon 13) of the ACY1 gene. This alteration results from a C to T substitution at nucleotide position 1057, causing the arginine (R) at amino acid position 353 to be replaced by a cysteine (C). Based on data from gnomAD, the T allele has an overall frequency of 0.27% (770/282836) total alleles studied, including 4 homozygotes. The highest observed frequency was 0.41% (534/129150) of European (non-Finnish) alleles. This variant has been reported in the homozygous and compound heterozygous state in several individuals with aminoacylase 1 deficiency (Van Coster, 2005; Sass, 2006; Sass, 2007; Tylki-Szymanska, 2010; Sass, 2015). In HEK293 cells, this variant demonstrated a loss of enzyme activity and no protein was detected by western blot compared to wild type (Sommer, 2011). Based on the available evidence, this alteration is classified as likely pathogenic. -

Inborn aminoacylase deficiency

Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Nov 29, 2023

The p.Arg353Cys variant in ACY1 has been reported in at least 5 homozygous and 2 compound heterozygous individuals with aminoacylase 1 deficiency, including one homozygous individual with an additional finding of Menkes disease (Tylki-Szymanska 2010 PMID: 20480396, Sass 2007 PMID: 17562838, Sass 2006 PMID: 16465618, van Coster 2005 PMID: 16274666, Mauri 2023 PMID: 36936426). There was little consistency in the phenotypes of these individuals or in the severity of the phenotypes, aside from some neurological involvement. This variant has also been It has also been reported by other clinical laboratories in ClinVar (Variation ID 18110) and has been identified in 0.39% (271/68042) European chromosomes by gnomAD (https://gnomad.broadinstitute.org/, v3.1.2), including in 4 homozygous individuals (v2.1.1). In vitro functional studies support an impact on protein function, where HEK cells with the variant show a loss of enzyme activity and no ACY1 protein detection on a western blot compared to wildtype (Sommer 2011 PMID: 21414403), and lymphoblast cell lines generated from a homozygous patient with this variant show <1% of normal aminoacylase I enzyme activity (van Coster 2005 PMID: 16274666). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In summary, this variant meets criteria to be classified as likely pathogenic for autosomal recessive aminoacylase 1 deficiency. ACMG/AMP criteria applied: PM3_Strong, PS3_Moderate. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.73

BayesDel_addAF

Benign

-0.020

BayesDel_noAF

Pathogenic

0.20

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Uncertain

0.57

.;D;.;.;.;D;.

Eigen

Uncertain

0.62

Eigen_PC

Uncertain

0.45

FATHMM_MKL

Uncertain

0.80

LIST_S2

Pathogenic

0.99

D;.;D;D;D;D;D

M_CAP

Uncertain

0.12

MetaRNN

Benign

0.037

T;T;T;T;T;T;T

MetaSVM

Uncertain

0.086

MutationAssessor

Pathogenic

3.8

.;H;.;.;.;H;.

PrimateAI

Uncertain

0.54

PROVEAN

Pathogenic

-7.8

D;.;D;D;D;D;.

REVEL

Uncertain

0.62

Sift

Pathogenic

0.0

D;.;D;D;D;D;.

Sift4G

Pathogenic

0.0010

D;.;D;D;D;D;.

Polyphen

1.0

.;D;.;.;.;D;.

Vest4

0.93

MVP

0.76

MPC

0.67

ClinPred

0.14

GERP RS

5.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

Varity_R

0.96

gMVP

0.95

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over