chr17-19663333-CCC-GGGCTAAAAGTACTGTTGGGG

Position:

• chr17-19663333-CCC-GGGCTAAAAGTACTGTTGGGG

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM2 PM4 PP3 PP5_Very_Strong

The NM_000382.3(ALDH3A2):​c.941_943delCCCinsGGGCTAAAAGTACTGTTGGGG​(p.Ala314_Pro315delinsGlyAlaLysSerThrValGlyAla) variant causes a missense, disruptive inframe insertion, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin Lovd.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ALDH3A2 NM_000382.3 missense, disruptive_inframe_insertion, splice_region
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:5
• 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]

ALDH3A2 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 13 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_000382.3.
• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
• PP5: Variant 17-19663333-CCC-GGGCTAAAAGTACTGTTGGGG is Pathogenic according to our data. Variant chr17-19663333-CCC-GGGCTAAAAGTACTGTTGGGG is described in ClinVar as [Pathogenic]. Clinvar id is 1638.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALDH3A2	NM_000382.3	c.941_943delCCCinsGGGCTAAAAGTACTGTTGGGG	p.Ala314_Pro315delinsGlyAlaLysSerThrValGlyAla	missense_variant, disruptive_inframe_insertion, splice_region_variant		ENST00000176643.11	NP_000373.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALDH3A2	ENST00000176643.11	c.941_943delCCCinsGGGCTAAAAGTACTGTTGGGG	p.Ala314_Pro315delinsGlyAlaLysSerThrValGlyAla	missense_variant, disruptive_inframe_insertion, splice_region_variant		1	NM_000382.3	ENSP00000176643.6

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Sjögren-Larsson syndrome Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 28, 2022	Variant summary: ALDH3A2 c.941_943delinsGGGCTAAAAGTACTGTTGGGG (p.Ala314_Pro315delinsGlyAlaLysSerThrValGlyAla) results in an in-frame deletion/insertion that is predicted to delete 2 amino acids and insert 8 amino acids into the encoded protein. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The frequency of this variant in the general population could not be determined as the technology used for large population databases (ExAC, gnomAD, ESP, 1000G) cannot detect variants of this type. c.941_943delinsGGGCTAAAAGTACTGTTGGGG has been reported in the literature in individuals affected with Sjogren-Larsson Syndrome or related disorders. These data indicate that the variant may be associated with disease. At least two publications report that FALDH activity in patients carrying this variant is <10% of normal activity. One clinical diagnostic laboratory has 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. -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Oct 08, 2024	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Sjogren-Larsson syndrome (MIM#270200). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0213 - In-frame insertion/deletion in a non-repetitive region that has high conservation. (SP) 0252 - This variant is homozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). However, as this is a complex variant it may be misannotated in gnomAD. There are several variants gnomAD v3 which, if combined, may be this variant (2 heterozygotes, 0 homozygotes). (SP) 0600 - Variant is located in the annotated aldehyde dehydrogenase family domain (DECIPHER). (I) 0704 - A missense variant involving one of the residues affected by the variant identified in this case has limited previous evidence for pathogenicity. p.(Pro315Ser) has been reported as pathogenic by multiple clinical laboratories in ClinVar. (SP) 0801 - This variant has strong previous evidence of pathogenic in unrelated individuals. This variant has been classified as pathogenic by a clinical laboratory in ClinVar, and has been observed in four individuals with Sjogren-Larsson syndrome in the literature (PMIDs: 8528251, 34531397, 9250352, 9829906). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. An individual homozygous for this variant was shown to have 8% of mean ALDH3A2 activity and their heterozygous parents had 39% and 47% of mean activity (PMID: 8528251). (SP) 1209 - This variant has been shown to be both maternally and paternally inherited (biallelic) (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Pathogenic, no assertion criteria provided	literature only	OMIM	May 01, 1997	- -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Mar 13, 2024	- -

Cerebral palsy Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Neurogenetics Research Program, University of Adelaide

Jun 10, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs730880264; hg19: chr17-19566646;