17-19663335-C-T

Position:

• chr17-19663335-C-T

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2 PP3_Strong PP5_Very_Strong

The NM_000382.3(ALDH3A2):​c.943C>T​(p.Pro315Ser) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000483 in 1,613,724 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000053 (0 hom.)
• Consequence: ALDH3A2 NM_000382.3 missense, splice_region
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:14
• Conservation: PhyloP100: 7.83

Genes affected

ALDH3A2 (HGNC:403): (aldehyde dehydrogenase 3 family member A2) Aldehyde dehydrogenase isozymes are thought to play a major role in the detoxification of aldehydes generated by alcohol metabolism and lipid peroxidation. This gene product catalyzes the oxidation of long-chain aliphatic aldehydes to fatty acid. Mutations in the gene cause Sjogren-Larsson syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.986
• PP5: Variant 17-19663335-C-T is Pathogenic according to our data. Variant chr17-19663335-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1640.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-19663335-C-T is described in Lovd as [Pathogenic]. Variant chr17-19663335-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALDH3A2	NM_000382.3	c.943C>T	p.Pro315Ser	missense_variant, splice_region_variant	7/10	ENST00000176643.11	NP_000373.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALDH3A2	ENST00000176643.11	c.943C>T	p.Pro315Ser	missense_variant, splice_region_variant	7/10	1	NM_000382.3	ENSP00000176643	P1

Frequencies

GnomAD3 genomes AF: 0.00000658 AC: 1 AN: 152032 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

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: 0.0000147

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000107 AC: 27 AN: 251342 Hom.: 0 AF XY: 0.0000810 AC XY: 11 AN XY: 135844

Gnomad AFR exome AF: 0.00

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: 0.0000462

Gnomad NFE exome AF: 0.000229

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000527 AC: 77 AN: 1461692 Hom.: 0 Cov.: 31 AF XY: 0.0000426 AC XY: 31 AN XY: 727152

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000936

Gnomad4 NFE exome AF: 0.0000558

Gnomad4 OTH exome AF: 0.000166

GnomAD4 genome AF: 0.00000658 AC: 1 AN: 152032 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 74264

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000422 Hom.: 0

Bravo AF: 0.0000151

ExAC AF: 0.000189 AC: 23

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:14

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:8

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 12, 2024	This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 315 of the ALDH3A2 protein (p.Pro315Ser). This variant is present in population databases (rs72547571, gnomAD 0.02%). This missense change has been observed in individuals with Sjögren-Larsson syndrome (SLS) (PMID: 9254849). It is commonly reported in individuals of northern Sweden ancestry (PMID: 9204959, 9254849, 10384396, 11408337, 19124283). ClinVar contains an entry for this variant (Variation ID: 1640). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 04, 2016	P315S has been reported previously in association with Sjögren-Larsson syndrome (SLS) and is a common pathogenic variant among individuals of northern European and Swedish ancestry (De Laurenzi et al., 1997). Expression studies demonstrated that this pathogenic variant leads to loss of enzymatic activity (De Laurenzi et al., 1997). -
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	Eurofins Ntd Llc (ga)	Jun 13, 2014	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

Sjögren-Larsson syndrome Pathogenic:6

Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	May 01, 1999	- -
Pathogenic, criteria provided, single submitter	research	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Dec 03, 2018	The homozygous p.Pro315Ser variant in ALDH3A2 was identified by our study in one individual with Sjoegren-Larsson syndrome. The p.Pro315Ser variant in ALDH3A2 has been reported in 41 Northern European individuals with Sjoegren-Larsson syndrome, segregated with disease in 2 affected relatives from 1 families (PMID: 9204959, 9254849, 10577908), and has been identified in 0.02132% (27/126636) of European (non-Finnish) chromosomes and 0.003880% (1/25772) of European (Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs72547571). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. The prevalence of the variant in affected Northern European individuals and data from large population studies suggests this is a founder variant with a higher prevalence than the prevalence of the variant in a control population (PMID: 9254849). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. The presence of this variant in combination with a reported likely pathogenic variant and in an individual with Sjoegren-Larsson syndrome increases the likelihood that the p.Pro315Ser variant is pathogenic (PMID: 10577908; Variation ID: 1643). Functional expression studies with baculovirus and mammalian ovary cells provide some evidence that the p.Pro315Ser variant may impact protein function (PMID: 9204959, 10577908). However, these types of assays may not accurately represent biological function. This variant has also been reported pathogenic in ClinVar (Variation ID: 1640). In summary, the p.Pro315Ser variant is pathogenic based off of our findings, multiple reports in ClinVar, and the literature. ACMG/AMP Criteria applied: PM2, PS3, PP3, PP1, PS4_Moderate (Richards 2015). -
Likely pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	May 09, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Nov 12, 2019	NM_000382.2(ALDH3A2):c.943C>T(P315S) is classified as pathogenic in the context of Sjogren-Larsson syndrome. Sources cited for classification include the following: PMID 10384396, 9254849, 9204959, 10577908, 9467812 and 11408337. Classification of NM_000382.2(ALDH3A2):c.943C>T(P315S) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 17, 2018	Variant summary: ALDH3A2 c.943C>T (p.Pro315Ser) results in a non-conservative amino acid change located in the Aldehyde dehydrogenase domain of 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 0.0001 in 277112 control chromosomes (gnomAD). The variant, c.943C>T, has been reported in the literature in multiple individuals affected with Sjogren-Larsson Syndrome, in particular in populations of Northern European descent (DeLaurenzi_1997). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity (DeLaurenzi_1997). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.89
BayesDel_addAF	Pathogenic	0.29	D
BayesDel_noAF	Pathogenic	0.48
CADD	Pathogenic	26
DANN	Benign	0.94
DEOGEN2	Pathogenic	0.90	.;D;.;D;.;D
Eigen	Pathogenic	0.98
Eigen_PC	Pathogenic	0.88
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Pathogenic	0.99	.;D;.;.;D;.
M_CAP	Pathogenic	0.35	D
MetaRNN	Pathogenic	0.99	D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	4.4	.;H;H;H;H;H
MutationTaster	Benign	1.0	A;A;A;A;A
PrimateAI	Uncertain	0.58	T
PROVEAN	Pathogenic	-7.8	.;D;.;D;D;.
REVEL	Pathogenic	0.97
Sift	Pathogenic	0.0	.;D;.;D;D;.
Sift4G	Uncertain	0.0020	D;D;D;D;D;D
Polyphen		1.0	.;D;D;D;D;D
Vest4		0.91
MutPred		0.94		Loss of sheet (P = 0.1158);Loss of sheet (P = 0.1158);Loss of sheet (P = 0.1158);Loss of sheet (P = 0.1158);Loss of sheet (P = 0.1158);Loss of sheet (P = 0.1158);
MVP		1.0
MPC		0.85
ClinPred		0.99	D
GERP RS		5.1
Varity_R		0.99
gMVP		0.97

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: rs72547571; hg19: chr17-19566648;