NM_000370.3(TTPA):c.372del (p.Val126fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 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:: RCV003712136.2

Allele description [Variation Report for NM_000370.3(TTPA):c.372del (p.Val126fs)]

NM_000370.3(TTPA):c.372del (p.Val126fs)

Gene:

TTPA:alpha tocopherol transfer protein [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

8q12.3

Genomic location:

Preferred name:

NM_000370.3(TTPA):c.372del (p.Val126fs)

HGVS:

NC_000008.11:g.63066087del
NG_016123.1:g.24970del
NM_000370.3:c.372delMANE SELECT
NM_001413414.1:c.205-1768del
NM_001413415.1:c.359-4659del
NM_001413416.1:c.372del
NM_001413417.1:c.205-4659del
NM_001413418.1:c.489del
NP_000361.1:p.Val126fs
NP_001400345.1:p.Val126fs
NP_001400347.1:p.Val165fs
NC_000008.10:g.63978643del
NC_000008.10:g.63978646del
NR_182150.1:n.539del
NR_182151.1:n.250del

Protein change:

V126fs

Molecular consequence:

NM_000370.3:c.372del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001413416.1:c.372del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001413418.1:c.489del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001413414.1:c.205-1768del - intron variant - [Sequence Ontology: SO:0001627]
NM_001413415.1:c.359-4659del - intron variant - [Sequence Ontology: SO:0001627]
NM_001413417.1:c.205-4659del - intron variant - [Sequence Ontology: SO:0001627]
NR_182150.1:n.539del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_182151.1:n.250del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: Homo sapiens NME/NM23 family member 5 (NME5), transcript variant X5, ...
PREDICTED: Homo sapiens NME/NM23 family member 5 (NME5), transcript variant X5, mRNA
gi|2217357584|ref|XM_047417806.1|

Nucleotide
PREDICTED: Homo sapiens NME/NM23 family member 5 (NME5), transcript variant X4, ...
PREDICTED: Homo sapiens NME/NM23 family member 5 (NME5), transcript variant X4, mRNA
gi|2217357582|ref|XM_047417805.1|

Nucleotide
PREDICTED: Homo sapiens NME/NM23 family member 5 (NME5), transcript variant X9, ...
PREDICTED: Homo sapiens NME/NM23 family member 5 (NME5), transcript variant X9, mRNA
gi|2462604655|ref|XM_054353620.1|

Nucleotide
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial (chloropl...
ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial (chloroplast) [Medicago sativa subsp. falcata]
gi|2618219188|gb|WOX62763.1|

Protein
Homo sapiens UBX domain protein 2B (UBXN2B), transcript variant 3, mRNA
Homo sapiens UBX domain protein 2B (UBXN2B), transcript variant 3, mRNA
gi|1388153474|ref|NM_001363181.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004475576	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 28, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 9463307, 26068213, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004475576

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 28, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Citations

PubMed

Ataxia with isolated vitamin E deficiency: heterogeneity of mutations and phenotypic variability in a large number of families.

Cavalier L, Ouahchi K, Kayden HJ, Di Donato S, Reutenauer L, Mandel JL, Koenig M.

Am J Hum Genet. 1998 Feb;62(2):301-10.

PubMed [citation]

PMID:: 9463307
PMCID:: PMC1376876

Molecular and clinical study of a cohort of 110 Algerian patients with autosomal recessive ataxia.

Hamza W, Ali Pacha L, Hamadouche T, Muller J, Drouot N, Ferrat F, Makri S, Chaouch M, Tazir M, Koenig M, Benhassine T.

BMC Med Genet. 2015 Jun 12;16:36. doi: 10.1186/s12881-015-0180-3.

PubMed [citation]

PMID:: 26068213
PMCID:: PMC4630839

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004475576.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Val126Phefs*10) in the TTPA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TTPA are known to be pathogenic (PMID: 9463307, 26068213). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TTPA-related conditions. For these reasons, this variant has been 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: Sep 29, 2024

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