NM_001370658.1(BTD):c.1372G>A (p.Ala458Thr) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Apr 4, 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:: RCV003476902.1

Allele description [Variation Report for NM_001370658.1(BTD):c.1372G>A (p.Ala458Thr)]

NM_001370658.1(BTD):c.1372G>A (p.Ala458Thr)

Gene:

BTD:biotinidase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p25.1

Genomic location:

Preferred name:

NM_001370658.1(BTD):c.1372G>A (p.Ala458Thr)

HGVS:

NC_000003.12:g.15645288G>A
NG_008019.2:g.48937G>A
NG_008019.3:g.48938G>A
NM_000060.4:c.1432G>A
NM_001281723.4:c.1372G>A
NM_001281724.3:c.1372G>A
NM_001281725.3:c.1372G>A
NM_001323582.2:c.1372G>A
NM_001370658.1:c.1372G>AMANE SELECT
NM_001370752.1:c.1015+357G>A
NM_001370753.1:c.399+3231G>A
NM_001407364.1:c.1372G>A
NM_001407365.1:c.1372G>A
NM_001407366.1:c.1372G>A
NM_001407367.1:c.1372G>A
NM_001407368.1:c.1372G>A
NM_001407369.1:c.1372G>A
NM_001407370.1:c.1372G>A
NM_001407371.1:c.1372G>A
NM_001407372.1:c.1372G>A
NM_001407373.1:c.1372G>A
NM_001407374.1:c.1372G>A
NM_001407375.1:c.1372G>A
NM_001407376.1:c.1372G>A
NM_001407377.1:c.1372G>A
NM_001407378.1:c.1372G>A
NP_000051.1:p.Ala478Thr
NP_001268652.2:p.Ala458Thr
NP_001268652.2:p.Ala458Thr
NP_001268653.2:p.Ala458Thr
NP_001268654.1:p.Ala458Thr
NP_001268654.1:p.Ala458Thr
NP_001310511.1:p.Ala458Thr
NP_001310511.1:p.Ala458Thr
NP_001357587.1:p.Ala458Thr
NP_001394293.1:p.Ala458Thr
NP_001394294.1:p.Ala458Thr
NP_001394295.1:p.Ala458Thr
NP_001394296.1:p.Ala458Thr
NP_001394297.1:p.Ala458Thr
NP_001394298.1:p.Ala458Thr
NP_001394299.1:p.Ala458Thr
NP_001394300.1:p.Ala458Thr
NP_001394301.1:p.Ala458Thr
NP_001394302.1:p.Ala458Thr
NP_001394303.1:p.Ala458Thr
NP_001394304.1:p.Ala458Thr
NP_001394305.1:p.Ala458Thr
NP_001394306.1:p.Ala458Thr
NP_001394307.1:p.Ala458Thr
NC_000003.11:g.15686795G>A
NM_001281723.3:c.1372G>A
NM_001281725.2:c.1372G>A
NM_001323582.1:c.1372G>A
NM_001370658.1:c.1372G>A

Protein change:

A458T

Links:

dbSNP: rs181396238

NCBI 1000 Genomes Browser:

rs181396238

Molecular consequence:

NM_001370752.1:c.1015+357G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001370753.1:c.399+3231G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000060.4:c.1432G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001281723.4:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001281724.3:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001281725.3:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001323582.2:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370658.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407364.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407365.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407366.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407367.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407368.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407369.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407370.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407371.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407372.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407373.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407374.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407375.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407376.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407377.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407378.1:c.1372G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Homo sapiens leupaxin (LPXN), transcript variant 2, mRNA
Homo sapiens leupaxin (LPXN), transcript variant 2, mRNA
gi|221316657|ref|NM_004811.2|

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gi|676614|gnl|dbEST|126549|gb|T6717

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004220739	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely pathogenic (Apr 4, 2023)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26810761, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004220739

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Likely pathogenic
(Apr 4, 2023)

unknown

clinical testing

PubMed (2)
[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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Forty-eight novel mutations causing biotinidase deficiency.

Procter M, Wolf B, Mao R.

Mol Genet Metab. 2016 Mar;117(3):369-72. doi: 10.1016/j.ymgme.2016.01.002. Epub 2016 Jan 12.

PubMed [citation]

PMID:: 26810761

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004220739.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

The frequency of this variant in the general population, 0.000008 (2/251444 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in an individual with biotinidase deficiency (PMID: 2681076 (2016)). Functional analysis demonstrated this variant to cause a low BTD serum level compared to a matched control (PMID: 2681076 (2016)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, this variant is classified as likely pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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