VCV003336588.3 - ClinVar

NM_016180.5(SLC45A2):c.1456G>A (p.Ala486Thr)

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.

(3)

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.

Pathogenic/Likely pathogenic

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_016180.5(SLC45A2):c.1456G>A (p.Ala486Thr)

Variation ID: 3336588 Accession: VCV003336588.3

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 5p13.2 5: 33944785 (GRCh38) [ NCBI UCSC ] 5: 33944890 (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	Aug 11, 2024	Nov 30, 2024	May 15, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_016180.5:c.1456G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_057264.4:p.Ala486Thr	missense
NM_016180.4:c.1456G>A
NC_000005.10:g.33944785C>T
NC_000005.9:g.33944890C>T
NG_011691.2:g.44891G>A
NG_011691.3:g.44908G>A
NG_104672.1:g.653C>T
NG_104673.1:g.152C>T

... more HGVS ... less HGVS

Protein change

A486T

Other names

Canonical SPDI

NC_000005.10:33944784: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.
SLC45A2		-	-	GRCh38 GRCh38 GRCh37	581	629

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.
Oculocutaneous albinism type 4	Pathogenic (1)	criteria provided, single submitter	May 15, 2024	RCV004689540.1
SLC45A2-related disorder	Likely pathogenic (1)	no assertion criteria provided	Aug 19, 2024	RCV004756575.1
Oculocutaneous albinism type 4 SKIN/HAIR/EYE PIGMENTATION 5, BLACK/NONBLACK HAIR	Likely pathogenic (1)	criteria provided, single submitter	-	RCV004796878.1

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.
Pathogenic (May 15, 2024)	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015) Method: clinical testing	Oculocutaneous albinism type 4 Affected status: unknown Allele origin: germline	Women's Health and Genetics/Laboratory Corporation of America, LabCorp Accession: SCV005185813.1 First in ClinVar: Aug 11, 2024 Last updated: Aug 11, 2024	Publications: PubMed (1) PubMed: 34838614 Comment: Variant summary: SLC45A2 c.1456G>A (p.Ala486Thr) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging … (more) Variant summary: SLC45A2 c.1456G>A (p.Ala486Thr) 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 was absent in 251166 control chromosomes. c.1456G>A has been reported in the literature in multiple individuals affected with albinism (example, Wei_2022). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 34838614). No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
Likely pathogenic (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Oculocutaneous albinism type 4 SKIN/HAIR/EYE PIGMENTATION 5, BLACK/NONBLACK HAIR Explanation for multiple conditions: Uncertain. The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. Affected status: yes Allele origin: germline	Juno Genomics, Hangzhou Juno Genomics, Inc Accession: SCV005418838.1 First in ClinVar: Nov 30, 2024 Last updated: Nov 30, 2024	Comment: PM2_Supporting+PP3_Moderate+PM5_Supporting+PM3_Supporting+PP4
Likely pathogenic (Aug 19, 2024)	no assertion criteria provided Method: clinical testing	SLC45A2-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV005363171.1 First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024	Comment: The SLC45A2 c.1456G>A variant is predicted to result in the amino acid substitution p.Ala486Thr. This variant has been reported in multiple individuals with oculocutaneous albinism … (more) The SLC45A2 c.1456G>A variant is predicted to result in the amino acid substitution p.Ala486Thr. This variant has been reported in multiple individuals with oculocutaneous albinism (Xue et al. 2016. PubMed ID: 27706749; Chuan et al. 2021. PubMed ID: 32552135 Wei. 2022. PubMed ID: 34838614). This variant has not been reported in a large population database, indicating this variant is rare. Given the evidence, we interpret this variant as likely pathogenic. (less)

Comment:

Variant summary: SLC45A2 c.1456G>A (p.Ala486Thr) 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 was absent in 251166 control chromosomes. c.1456G>A has been reported in the literature in multiple individuals affected with albinism (example, Wei_2022). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 34838614). No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as pathogenic.

Comment:

The SLC45A2 c.1456G>A variant is predicted to result in the amino acid substitution p.Ala486Thr. This variant has been reported in multiple individuals with oculocutaneous albinism (Xue et al. 2016. PubMed ID: 27706749; Chuan et al. 2021. PubMed ID: 32552135 Wei. 2022. PubMed ID: 34838614). This variant has not been reported in a large population database, indicating this variant is rare. Given the evidence, we interpret this variant as likely pathogenic.

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

Title	Author	Journal	Year	Link
Spectrum Analysis of Albinism Genes in a Large Cohort of Chinese Index Patients.	Wei A	The Journal of investigative dermatology	2022	PMID: 34838614

Text-mined citations for this variant ...

Record last updated Dec 07, 2024

ClinVar Genomic variation as it relates to human health

NM_016180.5(SLC45A2):c.1456G>A (p.Ala486Thr)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...