NM_001370658.1(BTD):c.1289A>C (p.His430Pro) AND Biotinidase deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 31, 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:: RCV002038794.7

Allele description [Variation Report for NM_001370658.1(BTD):c.1289A>C (p.His430Pro)]

NM_001370658.1(BTD):c.1289A>C (p.His430Pro)

Gene:

BTD:biotinidase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p25.1

Genomic location:

Preferred name:

NM_001370658.1(BTD):c.1289A>C (p.His430Pro)

HGVS:

NC_000003.12:g.15645205A>C
NG_008019.2:g.48854A>C
NG_008019.3:g.48855A>C
NM_000060.4:c.1349A>C
NM_001281723.4:c.1289A>C
NM_001281724.3:c.1289A>C
NM_001281725.3:c.1289A>C
NM_001323582.2:c.1289A>C
NM_001370658.1:c.1289A>CMANE SELECT
NM_001370752.1:c.1015+274A>C
NM_001370753.1:c.399+3148A>C
NM_001407364.1:c.1289A>C
NM_001407365.1:c.1289A>C
NM_001407366.1:c.1289A>C
NM_001407367.1:c.1289A>C
NM_001407368.1:c.1289A>C
NM_001407369.1:c.1289A>C
NM_001407370.1:c.1289A>C
NM_001407371.1:c.1289A>C
NM_001407372.1:c.1289A>C
NM_001407373.1:c.1289A>C
NM_001407374.1:c.1289A>C
NM_001407375.1:c.1289A>C
NM_001407376.1:c.1289A>C
NM_001407377.1:c.1289A>C
NM_001407378.1:c.1289A>C
NP_000051.1:p.His450Pro
NP_001268652.2:p.His430Pro
NP_001268652.2:p.His430Pro
NP_001268653.2:p.His430Pro
NP_001268654.1:p.His430Pro
NP_001268654.1:p.His430Pro
NP_001310511.1:p.His430Pro
NP_001310511.1:p.His430Pro
NP_001357587.1:p.His430Pro
NP_001394293.1:p.His430Pro
NP_001394294.1:p.His430Pro
NP_001394295.1:p.His430Pro
NP_001394296.1:p.His430Pro
NP_001394297.1:p.His430Pro
NP_001394298.1:p.His430Pro
NP_001394299.1:p.His430Pro
NP_001394300.1:p.His430Pro
NP_001394301.1:p.His430Pro
NP_001394302.1:p.His430Pro
NP_001394303.1:p.His430Pro
NP_001394304.1:p.His430Pro
NP_001394305.1:p.His430Pro
NP_001394306.1:p.His430Pro
NP_001394307.1:p.His430Pro
NC_000003.11:g.15686712A>C
NM_001281723.3:c.1289A>C
NM_001281725.2:c.1289A>C
NM_001323582.1:c.1289A>C

Protein change:

H430P

Links:

dbSNP: rs559136372

NCBI 1000 Genomes Browser:

rs559136372

Molecular consequence:

NM_001370752.1:c.1015+274A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001370753.1:c.399+3148A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000060.4:c.1349A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001281723.4:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001281724.3:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001281725.3:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001323582.2:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370658.1:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407364.1:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407365.1:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407366.1:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407367.1:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407368.1:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407369.1:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407370.1:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407371.1:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407372.1:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407373.1:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407374.1:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407375.1:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407376.1:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407377.1:c.1289A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407378.1:c.1289A>C - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002310305	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 31, 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

SCV002310305

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 31, 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, SCV002310305.3

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

Description

This variant has not been reported in the literature in individuals with BTD-related conditions. This variant is present in population databases (rs559136372, ExAC 0.01%). This sequence change replaces histidine with proline at codon 450 of the BTD protein (p.His450Pro). The histidine residue is moderately conserved and there is a moderate physicochemical difference between histidine and proline. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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: Sep 29, 2024

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