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NM_002778.4(PSAP):c.695G>A (p.Arg232His) AND Sphingolipid activator protein 1 deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 20, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001991035.5

Allele description [Variation Report for NM_002778.4(PSAP):c.695G>A (p.Arg232His)]

NM_002778.4(PSAP):c.695G>A (p.Arg232His)

Gene:
PSAP:prosaposin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q22.1
Genomic location:
Preferred name:
NM_002778.4(PSAP):c.695G>A (p.Arg232His)
HGVS:
  • NC_000010.11:g.71828039C>T
  • NG_009301.1:g.28287G>A
  • NM_001042465.3:c.695G>A
  • NM_001042466.3:c.695G>A
  • NM_002778.4:c.695G>AMANE SELECT
  • NP_001035930.1:p.Arg232His
  • NP_001035931.1:p.Arg232His
  • NP_002769.1:p.Arg232His
  • NC_000010.10:g.73587796C>T
Protein change:
R232H
Links:
dbSNP: rs147265566
NCBI 1000 Genomes Browser:
rs147265566
Molecular consequence:
  • NM_001042465.3:c.695G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001042466.3:c.695G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002778.4:c.695G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Sphingolipid activator protein 1 deficiency
Synonyms:
Metachromatic leukodystrophy due to saposin B deficiency; Metachromatic leukodystrophy due to cerebroside sulfatase activator deficiency; Saposin B Deficiency
Identifiers:
MONDO: MONDO:0009590; MedGen: C0268262; Orphanet: 512; OMIM: 249900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002261232Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 20, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002261232.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 232 of the PSAP protein (p.Arg232His). This variant is present in population databases (rs147265566, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with PSAP-related conditions. ClinVar contains an entry for this variant (Variation ID: 1479808). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The histidine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024