NM_002778.4(PSAP):c.1341C>A (p.Tyr447Ter) AND Combined PSAP deficiency

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 22, 2024
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:: RCV003484982.1

Allele description [Variation Report for NM_002778.4(PSAP):c.1341C>A (p.Tyr447Ter)]

NM_002778.4(PSAP):c.1341C>A (p.Tyr447Ter)

Genes:

CDH23:cadherin related 23 [Gene - OMIM - HGNC]
PSAP:prosaposin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q22.1

Genomic location:

Preferred name:

NM_002778.4(PSAP):c.1341C>A (p.Tyr447Ter)

HGVS:

NC_000010.11:g.71819474G>T
NG_009301.1:g.36852C>A
NM_001042465.3:c.1350C>A
NM_001042466.3:c.1347C>A
NM_002778.4:c.1341C>AMANE SELECT
NP_001035930.1:p.Tyr450Ter
NP_001035931.1:p.Tyr449Ter
NP_002769.1:p.Tyr447Ter
NC_000010.10:g.73579231G>T

Protein change:

Y447*

Molecular consequence:

NM_001042465.3:c.1350C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001042466.3:c.1347C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_002778.4:c.1341C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Combined PSAP deficiency (PSAPD)
Synonyms:: COMBINED SAP DEFICIENCY; PROSAPOSIN DEFICIENCY; Combined saposin deficiency; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012719; MedGen: C2673635; Orphanet: 139406; OMIM: 611721

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004232360	Department of Human Genetics, Hannover Medical School	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 22, 2024)	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

SCV004232360

Department of Human Genetics, Hannover Medical School

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 22, 2024)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Department of Human Genetics, Hannover Medical School, SCV004232360.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 4, 2024

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