NM_002778.4(PSAP):c.250-12_250-11del AND Sphingolipid activator protein 1 deficiency

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jul 9, 2023
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:: RCV003819098.2

Allele description [Variation Report for NM_002778.4(PSAP):c.250-12_250-11del]

NM_002778.4(PSAP):c.250-12_250-11del

Gene:

PSAP:prosaposin [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

10q22.1

Genomic location:

Preferred name:

NM_002778.4(PSAP):c.250-12_250-11del

HGVS:

NC_000010.11:g.71831262AC[1]
NG_009301.1:g.25061GT[1]
NM_001042465.3:c.250-12_250-11del
NM_001042466.3:c.250-12_250-11del
NM_002778.4:c.250-12_250-11delMANE SELECT
NC_000010.10:g.73591019AC[1]
NC_000010.10:g.73591019_73591020del

Molecular consequence:

NM_001042465.3:c.250-12_250-11del - intron variant - [Sequence Ontology: SO:0001627]
NM_001042466.3:c.250-12_250-11del - intron variant - [Sequence Ontology: SO:0001627]
NM_002778.4:c.250-12_250-11del - intron variant - [Sequence Ontology: SO:0001627]

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

Recent activity

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Caenorhabditis elegans Unclassified non-coding RNA F59G1.10 (F59G1.10), ncRNA
Caenorhabditis elegans Unclassified non-coding RNA F59G1.10 (F59G1.10), ncRNA
gi|392893011|ref|NR_051125.1|

Nucleotide
Caenorhabditis elegans NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit...
Caenorhabditis elegans NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 (Y71F9B.13), mRNA
gi|1972227228|ref|NM_058639.6|

Nucleotide
non-POU domain-containing octamer-binding protein isoform 2 [Homo sapiens]
non-POU domain-containing octamer-binding protein isoform 2 [Homo sapiens]
gi|224028248|ref|NP_001138882.1|

Protein
Tet [Trichoplusia ni]
Tet [Trichoplusia ni]
Gene ID:113502725

Gene
Trnav-uac [Trichoplusia ni]
Trnav-uac [Trichoplusia ni]
Gene ID:113502742

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004613848	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jul 9, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004613848

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jul 9, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV004613848.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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