chr1-113896264-AGTAATACAACAAAC-A

Variant names:

• chr1-113896264-AGTAATACAACAAAC-A
• rs1553257236
• NM_001253852.3:c.1490_1503delGTTTGTTGTATTAC

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1 PP5_Moderate

The NM_001253852.3(AP4B1):​c.1490_1503delGTTTGTTGTATTAC​(p.Arg497LeufsTer26) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: AP4B1 NM_001253852.3 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 9.29
• Publications: 0 publications found

Genes affected

AP4B1 (HGNC:572): (adaptor related protein complex 4 subunit beta 1) This gene encodes a subunit of a heterotetrameric adapter-like complex 4 that is involved in targeting proteins from the trans-Golgi network to the endosomal-lysosomal system. Mutations in this gene are associated with cerebral palsy spastic quadriplegic type 5 (CPSQ5) disorder. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

AP4B1-AS1 (HGNC:44114): (AP4B1 antisense RNA 1)

ACMG classification

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PP5: Variant 1-113896264-AGTAATACAACAAAC-A is Pathogenic according to our data. Variant chr1-113896264-AGTAATACAACAAAC-A is described in ClinVar as Pathogenic. ClinVar VariationId is 434228.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001253852.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AP4B1	NM_001253852.3	MANE Select	c.1490_1503delGTTTGTTGTATTAC	p.Arg497LeufsTer26	frameshift	Exon 8 of 10	NP_001240781.1	Q9Y6B7-1
	AP4B1	NM_001438373.1		c.1490_1503delGTTTGTTGTATTAC	p.Arg497LeufsTer26	frameshift	Exon 9 of 11	NP_001425302.1
	AP4B1	NM_006594.5		c.1490_1503delGTTTGTTGTATTAC	p.Arg497LeufsTer26	frameshift	Exon 9 of 11	NP_006585.2	Q9Y6B7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AP4B1	ENST00000369569.6	TSL:1 MANE Select	c.1490_1503delGTTTGTTGTATTAC	p.Arg497LeufsTer26	frameshift	Exon 8 of 10	ENSP00000358582.1	Q9Y6B7-1
	AP4B1	ENST00000256658.8	TSL:1	c.1490_1503delGTTTGTTGTATTAC	p.Arg497LeufsTer26	frameshift	Exon 9 of 11	ENSP00000256658.4	Q9Y6B7-1
	AP4B1	ENST00000863127.1		c.1616_1629delGTTTGTTGTATTAC	p.Arg539LeufsTer26	frameshift	Exon 9 of 11	ENSP00000533186.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	-	Hereditary spastic paraplegia 47 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		9.3
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1553257236; hg19: chr1-114438886;