NM_004722.4(AP4M1):c.568del (p.Asp190fs) AND Hereditary spastic paraplegia 50

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 28, 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:: RCV003479661.1

Allele description [Variation Report for NM_004722.4(AP4M1):c.568del (p.Asp190fs)]

NM_004722.4(AP4M1):c.568del (p.Asp190fs)

Gene:

AP4M1:adaptor related protein complex 4 subunit mu 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

7q22.1

Genomic location:

Preferred name:

NM_004722.4(AP4M1):c.568del (p.Asp190fs)

HGVS:

NC_000007.14:g.100104116del
NG_016312.1:g.7610del
NM_001363671.2:c.589del
NM_004722.4:c.568delMANE SELECT
NP_001350600.1:p.Asp197fs
NP_004713.2:p.Asp190fs
NC_000007.13:g.99701739del
NM_004722.4:c.568delGMANE SELECT

Protein change:

D190fs

Molecular consequence:

NM_001363671.2:c.589del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004722.4:c.568del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Hereditary spastic paraplegia 50 (SPG50)
Synonyms:: Spastic paraplegia 50, autosomal recessive
Identifiers:: MONDO: MONDO:0013048; MedGen: C2752008; Orphanet: 280763; OMIM: 612936

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004223226	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (Nov 28, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004223226

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Pathogenic
(Nov 28, 2023)

germline

clinical testing

Citation Link

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004223226.1

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

Description

Variant summary: AP4M1 c.568delG (p.Asp190MetfsX9) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 1.2e-05 in 251392 control chromosomes. To our knowledge, no occurrence of c.568delG in individuals affected with Hereditary Spastic Paraplegia 50 and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic.

#	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: Jan 6, 2024

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