NM_001370658.1(BTD):c.340T>C (p.Ser114Pro) AND Biotinidase deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 18, 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:: RCV002594004.2

Allele description [Variation Report for NM_001370658.1(BTD):c.340T>C (p.Ser114Pro)]

NM_001370658.1(BTD):c.340T>C (p.Ser114Pro)

Gene:

BTD:biotinidase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p25.1

Genomic location:

Preferred name:

NM_001370658.1(BTD):c.340T>C (p.Ser114Pro)

HGVS:

NC_000003.12:g.15641998T>C
NG_008019.2:g.45647T>C
NG_008019.3:g.45648T>C
NM_000060.4:c.400T>C
NM_001281723.4:c.340T>C
NM_001281724.3:c.340T>C
NM_001281725.3:c.340T>C
NM_001281726.3:c.340T>C
NM_001323582.2:c.340T>C
NM_001370658.1:c.340T>CMANE SELECT
NM_001370752.1:c.340T>C
NM_001370753.1:c.340T>C
NM_001407364.1:c.340T>C
NM_001407365.1:c.340T>C
NM_001407366.1:c.340T>C
NM_001407367.1:c.340T>C
NM_001407368.1:c.340T>C
NM_001407369.1:c.340T>C
NM_001407370.1:c.340T>C
NM_001407371.1:c.340T>C
NM_001407372.1:c.340T>C
NM_001407373.1:c.340T>C
NM_001407374.1:c.340T>C
NM_001407375.1:c.340T>C
NM_001407376.1:c.340T>C
NM_001407377.1:c.340T>C
NM_001407378.1:c.340T>C
NM_001407379.1:c.340T>C
NM_001407380.1:c.340T>C
NM_001407381.1:c.403T>C
NM_001407382.1:c.340T>C
NM_001407383.1:c.340T>C
NM_001407384.1:c.340T>C
NM_001407386.1:c.340T>C
NM_001407388.1:c.340T>C
NM_001407390.1:c.340T>C
NM_001407392.1:c.340T>C
NM_001407394.1:c.340T>C
NM_001407395.1:c.340T>C
NM_001407396.1:c.340T>C
NM_001407397.1:c.340T>C
NM_001407398.1:c.340T>C
NM_001407399.1:c.340T>C
NM_001407400.1:c.340T>C
NM_001407401.1:c.340T>C
NP_000051.1:p.Ser134Pro
NP_001268652.2:p.Ser114Pro
NP_001268652.2:p.Ser114Pro
NP_001268653.2:p.Ser114Pro
NP_001268654.1:p.Ser114Pro
NP_001268654.1:p.Ser114Pro
NP_001268655.2:p.Ser114Pro
NP_001268655.2:p.Ser114Pro
NP_001310511.1:p.Ser114Pro
NP_001310511.1:p.Ser114Pro
NP_001357587.1:p.Ser114Pro
NP_001357681.1:p.Ser114Pro
NP_001357682.1:p.Ser114Pro
NP_001394293.1:p.Ser114Pro
NP_001394294.1:p.Ser114Pro
NP_001394295.1:p.Ser114Pro
NP_001394296.1:p.Ser114Pro
NP_001394297.1:p.Ser114Pro
NP_001394298.1:p.Ser114Pro
NP_001394299.1:p.Ser114Pro
NP_001394300.1:p.Ser114Pro
NP_001394301.1:p.Ser114Pro
NP_001394302.1:p.Ser114Pro
NP_001394303.1:p.Ser114Pro
NP_001394304.1:p.Ser114Pro
NP_001394305.1:p.Ser114Pro
NP_001394306.1:p.Ser114Pro
NP_001394307.1:p.Ser114Pro
NP_001394308.1:p.Ser114Pro
NP_001394309.1:p.Ser114Pro
NP_001394310.1:p.Ser135Pro
NP_001394311.1:p.Ser114Pro
NP_001394312.1:p.Ser114Pro
NP_001394313.1:p.Ser114Pro
NP_001394315.1:p.Ser114Pro
NP_001394317.1:p.Ser114Pro
NP_001394319.1:p.Ser114Pro
NP_001394321.1:p.Ser114Pro
NP_001394323.1:p.Ser114Pro
NP_001394324.1:p.Ser114Pro
NP_001394325.1:p.Ser114Pro
NP_001394326.1:p.Ser114Pro
NP_001394327.1:p.Ser114Pro
NP_001394328.1:p.Ser114Pro
NP_001394329.1:p.Ser114Pro
NP_001394330.1:p.Ser114Pro
NC_000003.11:g.15683505T>C
NM_001281723.3:c.340T>C
NM_001281725.2:c.340T>C
NM_001281726.2:c.340T>C
NM_001323582.1:c.340T>C

Protein change:

S114P

Molecular consequence:

NM_000060.4:c.400T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001281723.4:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001281724.3:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001281725.3:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001281726.3:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001323582.2:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370658.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370752.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370753.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407364.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407365.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407366.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407367.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407368.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407369.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407370.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407371.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407372.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407373.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407374.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407375.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407376.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407377.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407378.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407379.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407380.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407381.1:c.403T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407382.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407383.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407384.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407386.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407388.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407390.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407392.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407394.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407395.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407396.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407397.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407398.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407399.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407400.1:c.340T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407401.1:c.340T>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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RNA polymerase sigma factor, sigma-54 family [Chlamydia pneumoniae AR39]
RNA polymerase sigma factor, sigma-54 family [Chlamydia pneumoniae AR39]
gi|8163554|gb|AAF73732.1||gnl|TIGR| 1

Protein
del(6q21)
del(6q21)

MedGen
Deletion 1p36
Deletion 1p36

MedGen
del(17p13)
del(17p13)

MedGen
del(10q24q25)
del(10q24q25)

MedGen

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002952575	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 18, 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

SCV002952575

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 18, 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, SCV002952575.1

#	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 serine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 134 of the BTD protein (p.Ser134Pro). This variant is present in population databases (rs759266571, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with BTD-related conditions. 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 proline 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: Sep 29, 2024

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