NM_001253852.3(AP4B1):c.-2_4delinsGCCA (p.Met1fs) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 16, 2019
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:: RCV001192870.9

Allele description [Variation Report for NM_001253852.3(AP4B1):c.-2_4delinsGCCA (p.Met1fs)]

NM_001253852.3(AP4B1):c.-2_4delinsGCCA (p.Met1fs)

Genes:

LOC129931235:ATAC-STARR-seq lymphoblastoid active region 1540 [Gene]
DCLRE1B:DNA cross-link repair 1B [Gene - OMIM - HGNC]
AP4B1:adaptor related protein complex 4 subunit beta 1 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

1p13.2

Genomic location:

Preferred name:

NM_001253852.3(AP4B1):c.-2_4delinsGCCA (p.Met1fs)

HGVS:

NC_000001.11:g.113904714_113904719delinsTGGC
NG_031901.1:g.5401_5406delinsGCCA
NG_057565.1:g.5096_5101delinsTGGC
NG_164279.1:g.240_245delinsTGGC
NM_001253852.3:c.-2_4delinsGCCAMANE SELECT
NM_001253853.3:c.-171_-166delinsGCCA
NM_001308312.2:c.-2_4delinsGCCA
NM_001319947.2:c.-331+6_-331+11delinsTGGC
NM_006594.5:c.-2_4delinsGCCA
NP_001240781.1:p.Met1fs
NP_001295241.1:p.Met1fs
NP_006585.2:p.Met1fs
LRG_1219:g.5096_5101delinsTGGC
NC_000001.10:g.114447336_114447341delinsTGGC
NM_006594.2:c.-2_4delAGATGCinsGCCA
NM_006594.4:c.-2_4delinsGCCA

Protein change:

M1fs

Links:

dbSNP: rs1558100393

NCBI 1000 Genomes Browser:

rs1558100393

Molecular consequence:

NM_001253853.3:c.-171_-166delinsGCCA - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001253852.3:c.-2_4delinsGCCA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001308312.2:c.-2_4delinsGCCA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_006594.5:c.-2_4delinsGCCA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001253852.3:c.-2_4delinsGCCA - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001308312.2:c.-2_4delinsGCCA - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_006594.5:c.-2_4delinsGCCA - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001319947.2:c.-331+6_-331+11delinsTGGC - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001361294	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Sep 16, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001361294

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Sep 16, 2019)

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, SCV001361294.2

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

Description

Variant summary: AP4B1 c.-2_4delinsGCCA (NA) alters the initiation codon and is predicted to result either in absence of the protein or truncation of the encoded protein due to translation initiation at a downstream codon. The variant was absent in 251448 control chromosomes (gnomAD). To our knowledge, no occurrence of c.-2_4delinsGCCA in individuals affected with Spastic paraplegia 47, autosomal recessive and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as VUS-possibly 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: Nov 24, 2024

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