VCV001367986.7 - ClinVar

NM_005050.4(ABCD4):c.1609C>A (p.Leu537Ile)

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.

(2)

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.

Uncertain significance

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_005050.4(ABCD4):c.1609C>A (p.Leu537Ile)

Variation ID: 1367986 Accession: VCV001367986.7

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 14q24.3 14: 74287837 (GRCh38) [ NCBI UCSC ] 14: 74754540 (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 28, 2022	Aug 11, 2024	Apr 15, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_005050.4:c.1609C>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_005041.1:p.Leu537Ile	missense
NM_001353591.2:c.1483C>A	NP_001340520.1:p.Leu495Ile	missense
NM_001353592.2:c.1483C>A	NP_001340521.1:p.Leu495Ile	missense
NM_001353593.2:c.1348C>A	NP_001340522.1:p.Leu450Ile	missense
NM_001353594.2:c.1297C>A	NP_001340523.1:p.Leu433Ile	missense
NM_001353595.2:c.1195C>A	NP_001340524.1:p.Leu399Ile	missense
NM_001353596.2:c.1195C>A	NP_001340525.1:p.Leu399Ile	missense
NM_001353597.2:c.1144C>A	NP_001340526.1:p.Leu382Ile	missense
NM_001353598.2:c.1132C>A	NP_001340527.1:p.Leu378Ile	missense
NM_001353599.2:c.1132C>A	NP_001340528.1:p.Leu378Ile	missense
NM_001353600.2:c.1132C>A	NP_001340529.1:p.Leu378Ile	missense
NM_001353601.2:c.1132C>A	NP_001340530.1:p.Leu378Ile	missense
NM_001353602.2:c.820C>A	NP_001340531.1:p.Leu274Ile	missense
NM_001353603.2:c.820C>A	NP_001340532.1:p.Leu274Ile	missense
NM_001353604.2:c.820C>A	NP_001340533.1:p.Leu274Ile	missense
NM_001353605.2:c.820C>A	NP_001340534.1:p.Leu274Ile	missense
NM_001353606.2:c.820C>A	NP_001340535.1:p.Leu274Ile	missense
NM_001353607.2:c.820C>A	NP_001340536.1:p.Leu274Ile	missense
NM_001353608.2:c.820C>A	NP_001340537.1:p.Leu274Ile	missense
NM_001353609.2:c.820C>A	NP_001340538.1:p.Leu274Ile	missense
NM_001353610.2:c.876C>A	NP_001340539.1:p.Asp292Glu	missense
NM_005050.3:c.1609C>A
NM_020324.3:c.1132C>A	NP_064720.1:p.Leu378Ile	missense
NM_020325.3:c.1609C>A	NP_064730.1:p.Leu537Ile	missense
NR_003256.3:n.1503C>A		non-coding transcript variant
NR_148466.2:n.1439C>A		non-coding transcript variant
NR_148467.2:n.1220C>A		non-coding transcript variant
NR_148468.2:n.1197C>A		non-coding transcript variant
NR_148469.2:n.1444C>A		non-coding transcript variant
NR_148470.2:n.1406C>A		non-coding transcript variant
NR_148471.2:n.1444C>A		non-coding transcript variant
NR_148472.2:n.1493C>A		non-coding transcript variant
NR_148473.2:n.1420C>A		non-coding transcript variant
NR_148474.2:n.1539C>A		non-coding transcript variant
NC_000014.9:g.74287837G>T
NC_000014.8:g.74754540G>T
NG_032875.1:g.20228C>A

... more HGVS ... less HGVS

Protein change

L378I, L495I, D292E, L537I, L450I, L274I, L382I, L399I, L433I

Other names

Canonical SPDI

NC_000014.9:74287836:G: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.

The Genome Aggregation Database (gnomAD) 0.00001

Links

dbSNP: rs780846855 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.
ABCD4		-	-	GRCh38 GRCh37	430	452

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.
Methylmalonic acidemia with homocystinuria, type cblJ	Uncertain significance (1)	criteria provided, single submitter	Jun 13, 2021	RCV001894526.6
Inborn genetic diseases	Uncertain significance (1)	criteria provided, single submitter	Apr 15, 2024	RCV004651760.1

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.
Uncertain significance (Jun 13, 2021)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Methylmalonic acidemia with homocystinuria, type cblJ Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV002136389.3 First in ClinVar: Mar 28, 2022 Last updated: Feb 28, 2024	Comment: 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 … (more) 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with ABCD4-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with isoleucine at codon 537 of the ABCD4 protein (p.Leu537Ile). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and isoleucine. (less)
Uncertain significance (Apr 15, 2024)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Inborn genetic diseases Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV005152235.1 First in ClinVar: Aug 11, 2024 Last updated: Aug 11, 2024	Comment: The c.1609C>A (p.L537I) alteration is located in exon 17 (coding exon 17) of the ABCD4 gene. This alteration results from a C to A substitution … (more) The c.1609C>A (p.L537I) alteration is located in exon 17 (coding exon 17) of the ABCD4 gene. This alteration results from a C to A substitution at nucleotide position 1609, causing the leucine (L) at amino acid position 537 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less)

Comment:

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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with ABCD4-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with isoleucine at codon 537 of the ABCD4 protein (p.Leu537Ile). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and isoleucine.

Comment:

The c.1609C>A (p.L537I) alteration is located in exon 17 (coding exon 17) of the ABCD4 gene. This alteration results from a C to A substitution at nucleotide position 1609, causing the leucine (L) at amino acid position 537 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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 rs780846855 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_005050.4(ABCD4):c.1609C>A (p.Leu537Ile)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs780846855 ...