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NM_002778.4(PSAP):c.816_823del (p.Asp272fs) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 8, 2019
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001254872.2

Allele description [Variation Report for NM_002778.4(PSAP):c.816_823del (p.Asp272fs)]

NM_002778.4(PSAP):c.816_823del (p.Asp272fs)

Gene:
PSAP:prosaposin [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
10q22.1
Genomic location:
Preferred name:
NM_002778.4(PSAP):c.816_823del (p.Asp272fs)
HGVS:
  • NC_000010.11:g.71821966_71821973del
  • NG_009301.1:g.34357_34364del
  • NM_001042465.3:c.825_832del
  • NM_001042466.3:c.822_829del
  • NM_002778.4:c.816_823delMANE SELECT
  • NP_001035930.1:p.Asp275fs
  • NP_001035931.1:p.Asp274fs
  • NP_002769.1:p.Asp272fs
  • NC_000010.10:g.73581719_73581726del
  • NC_000010.10:g.73581723_73581730del
  • NM_002778.3:c.816_823del
  • p.Asp272Glufs*29
Protein change:
D272fs
Links:
dbSNP: rs1244889985
NCBI 1000 Genomes Browser:
rs1244889985
Molecular consequence:
  • NM_001042465.3:c.825_832del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001042466.3:c.822_829del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_002778.4:c.816_823del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001427071Clinical Genomics Laboratory, Stanford Medicine
no assertion criteria provided
Likely pathogenic
(Aug 8, 2019) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From Clinical Genomics Laboratory, Stanford Medicine, SCV001427071.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedclinical testingnot provided

Description

The p.Asp272Glufs*29 variant in the PSAP gene has not been previously reported in association with disease. This variant has been identified in 1/16,256 African chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org/).The p.Asp272Glufs*29 variant results in a 8bp deletion, which causes a shift in the protein reading frame, leading to a premature termination codon 29 amino acids downstream. Loss of function is an established mechanism of disease for the PSAP gene. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the p.Asp272Glufs*29 variant as likely pathogenic for saposin deficiencies in an autosomal recessive manner based on the information above. [ACMG evidence codes used: PVS1; PM2]

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

Last Updated: Sep 29, 2024