VCV002442791.1 - ClinVar

NM_000691.5(ALDH3A1):c.703G>A (p.Gly235Arg)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Likely pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000691.5(ALDH3A1):c.703G>A (p.Gly235Arg)

Variation ID: 2442791 Accession: VCV002442791.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 17p11.2 17: 19741197 (GRCh38) [ NCBI UCSC ] 17: 19644510 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Mar 11, 2023	Mar 11, 2023	Feb 25, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_000691.5:c.703G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000682.3:p.Gly235Arg	missense
NM_001135167.1:c.703G>A	NP_001128639.1:p.Gly235Arg	missense
NM_001135168.1:c.703G>A	NP_001128640.1:p.Gly235Arg	missense
NM_001330150.2:c.484G>A	NP_001317079.1:p.Gly162Arg	missense
NC_000017.11:g.19741197C>T
NC_000017.10:g.19644510C>T
NG_012251.1:g.12237G>A

... more HGVS ... less HGVS

Protein change

G162R, G235R

Other names

Canonical SPDI

NC_000017.11:19741196:C:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
ALDH3A1		-	-	GRCh38 GRCh37	30	141

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Keratoconus	Likely pathogenic (1)	no assertion criteria provided	Feb 25, 2023	RCV003150597.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely pathogenic (Feb 25, 2023)	no assertion criteria provided Method: case-control	Keratoconus (Autosomal dominant inheritance) Affected status: yes Allele origin: inherited	Refractive Surgery Department, Bright Eye Hospital Accession: SCV003804500.1 First in ClinVar: Mar 11, 2023 Last updated: Mar 11, 2023	Comment: ALDH3A1 is thought to be involved in KC etiology.12-14 ALDH3A1 variants, rs1042183 and rs2228100, are strongly associated with KC in the Polish and Korean populations.12, … (more) ALDH3A1 is thought to be involved in KC etiology.12-14 ALDH3A1 variants, rs1042183 and rs2228100, are strongly associated with KC in the Polish and Korean populations.12, 14 The association of ALDH3A1 with intraocular pressure15 and refractive astigmatism16, 17 have also been observed. Furthermore, the relationship between astigmatism and KC has been reported, as 14.1% of patients with more than 2D astigmatism suffer from KC.18 Our findings further demonstrated the association of ALDH3A1 with KC. A novel SNP in ALDH3A1 was detected, g.19644510G>A, (c.703G>A, p.Gly235Arg [rs761232139]), causing a p.G235R amino acid change. This variant is located in exon 6 of ALDH3A1 gene and is predicted as highly conserved among species and probably damaging. The variant was identified in all KC members from the family 2, which means that rs761232139 may be a risk factor for KC and inherited in a dominant model. The residue was considered as a distinct structural and/or functional sequence of ALDH3A1, which is adjacent to the active site Cys-243. (less) Number of individuals with the variant: 3 Age: 22-44 years Sex: mixed Ethnicity/Population group: Han Geographic origin: China Comment on evidence: The proband (II.3) was a 22-year-old male. His UDVAs were 10/50 in both eyes and CDVA was 20/50 (right eye) with -3.50 DS/-4.00 DC × … (more) The proband (II.3) was a 22-year-old male. His UDVAs were 10/50 in both eyes and CDVA was 20/50 (right eye) with -3.50 DS/-4.00 DC × 175° and 20/20 (left eye) with -2.50 DS/-2.00 DC × 5°. The mean PEC and CCT were 61 and 481 µm in the right eye and 20 and 530 µm in the left eye (Fig. 3). Central cornea thinning, inferior steepening, bulging outwards, and irregular astigmatism were observed in both eyes of all three subjects. (less)

Comment:

ALDH3A1 is thought to be involved in KC etiology.12-14 ALDH3A1 variants, rs1042183 and rs2228100, are strongly associated with KC in the Polish and Korean populations.12, 14 The association of ALDH3A1 with intraocular pressure15 and refractive astigmatism16, 17 have also been observed. Furthermore, the relationship between astigmatism and KC has been reported, as 14.1% of patients with more than 2D astigmatism suffer from KC.18 Our findings further demonstrated the association of ALDH3A1 with KC. A novel SNP in ALDH3A1 was detected, g.19644510G>A, (c.703G>A, p.Gly235Arg [rs761232139]), causing a p.G235R amino acid change. This variant is located in exon 6 of ALDH3A1 gene and is predicted as highly conserved among species and probably damaging. The variant was identified in all KC members from the family 2, which means that rs761232139 may be a risk factor for KC and inherited in a dominant model. The residue was considered as a distinct structural and/or functional sequence of ALDH3A1, which is adjacent to the active site Cys-243.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Jun 23, 2024

ClinVar Genomic variation as it relates to human health

NM_000691.5(ALDH3A1):c.703G>A (p.Gly235Arg)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...