NM_001370658.1(BTD):c.1264G>A (p.Val422Ile) AND Biotinidase deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 1, 2021
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:: RCV001036979.8

Allele description [Variation Report for NM_001370658.1(BTD):c.1264G>A (p.Val422Ile)]

NM_001370658.1(BTD):c.1264G>A (p.Val422Ile)

Gene:

BTD:biotinidase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p25.1

Genomic location:

Preferred name:

NM_001370658.1(BTD):c.1264G>A (p.Val422Ile)

HGVS:

NC_000003.12:g.15645180G>A
NG_008019.2:g.48829G>A
NG_008019.3:g.48830G>A
NM_001281723.4:c.1264G>A
NM_001281724.3:c.1264G>A
NM_001281725.3:c.1264G>A
NM_001281726.2:c.*3042G>A
NM_001323582.2:c.1264G>A
NM_001370658.1:c.1264G>AMANE SELECT
NM_001370752.1:c.1015+249G>A
NM_001370753.1:c.399+3123G>A
NM_001407364.1:c.1264G>A
NM_001407365.1:c.1264G>A
NM_001407366.1:c.1264G>A
NM_001407367.1:c.1264G>A
NM_001407368.1:c.1264G>A
NM_001407369.1:c.1264G>A
NM_001407370.1:c.1264G>A
NM_001407371.1:c.1264G>A
NM_001407372.1:c.1264G>A
NM_001407373.1:c.1264G>A
NM_001407374.1:c.1264G>A
NM_001407375.1:c.1264G>A
NM_001407376.1:c.1264G>A
NM_001407377.1:c.1264G>A
NM_001407378.1:c.1264G>A
NM_001407379.1:c.1015+249G>A
NM_001407380.1:c.399+3123G>A
NM_001407398.1:c.399+3123G>A
NM_001407399.1:c.399+3123G>A
NM_001407400.1:c.399+3123G>A
NM_001407401.1:c.399+3123G>A
NP_001268652.2:p.Val422Ile
NP_001268653.2:p.Val422Ile
NP_001268654.1:p.Val422Ile
NP_001310511.1:p.Val422Ile
NP_001357587.1:p.Val422Ile
NP_001394293.1:p.Val422Ile
NP_001394294.1:p.Val422Ile
NP_001394295.1:p.Val422Ile
NP_001394296.1:p.Val422Ile
NP_001394297.1:p.Val422Ile
NP_001394298.1:p.Val422Ile
NP_001394299.1:p.Val422Ile
NP_001394300.1:p.Val422Ile
NP_001394301.1:p.Val422Ile
NP_001394302.1:p.Val422Ile
NP_001394303.1:p.Val422Ile
NP_001394304.1:p.Val422Ile
NP_001394305.1:p.Val422Ile
NP_001394306.1:p.Val422Ile
NP_001394307.1:p.Val422Ile
NC_000003.11:g.15686687G>A
NM_000060.3:c.1324G>A

Protein change:

V422I

Links:

dbSNP: rs776369447

NCBI 1000 Genomes Browser:

rs776369447

Molecular consequence:

NM_001370752.1:c.1015+249G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001370753.1:c.399+3123G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407379.1:c.1015+249G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407380.1:c.399+3123G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407398.1:c.399+3123G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407399.1:c.399+3123G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407400.1:c.399+3123G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407401.1:c.399+3123G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001281723.4:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001281724.3:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001281725.3:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001323582.2:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370658.1:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407364.1:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407365.1:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407366.1:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407367.1:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407368.1:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407369.1:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407370.1:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407371.1:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407372.1:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407373.1:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407374.1:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407375.1:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407376.1:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407377.1:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407378.1:c.1264G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Biotinidase deficiency
Synonyms:: BTD deficiency; Late-onset biotin-responsive multiple carboxylase deficiency; Biotin deficiency
Identifiers:: MONDO: MONDO:0009665; MedGen: C0220754; Orphanet: 79241; OMIM: 253260

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Molecular Structure
Molecular Structure
The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.<br/>Year introduced: 1989

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001200370	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 1, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001200370

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 1, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001200370.4

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

Description

This sequence change replaces valine with isoleucine at codon 442 of the BTD protein (p.Val442Ile). The valine residue is moderately conserved and there is a small physicochemical difference between valine and isoleucine. This variant is present in population databases (rs776369447, ExAC 0.06%). This variant has not been reported in the literature in individuals affected with BTD-related conditions. ClinVar contains an entry for this variant (Variation ID: 289111). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The isoleucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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 3, 2024

ClinVar

Relating variation to medicine