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NM_001370658.1(BTD):c.1177G>A (p.Gly393Ser) AND Biotinidase deficiency

Germline classification:
Uncertain significance (3 submissions)
Last evaluated:
Dec 5, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000032020.10

Allele description [Variation Report for NM_001370658.1(BTD):c.1177G>A (p.Gly393Ser)]

NM_001370658.1(BTD):c.1177G>A (p.Gly393Ser)

Gene:
BTD:biotinidase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p25.1
Genomic location:
Preferred name:
NM_001370658.1(BTD):c.1177G>A (p.Gly393Ser)
Other names:
G413S; p.Gly413Ser
HGVS:
  • NC_000003.12:g.15645093G>A
  • NG_008019.2:g.48742G>A
  • NG_008019.3:g.48743G>A
  • NM_000060.4:c.1237G>A
  • NM_001281723.4:c.1177G>A
  • NM_001281724.3:c.1177G>A
  • NM_001281725.3:c.1177G>A
  • NM_001323582.2:c.1177G>A
  • NM_001370658.1:c.1177G>AMANE SELECT
  • NM_001370752.1:c.1015+162G>A
  • NM_001370753.1:c.399+3036G>A
  • NM_001407364.1:c.1177G>A
  • NM_001407365.1:c.1177G>A
  • NM_001407366.1:c.1177G>A
  • NM_001407367.1:c.1177G>A
  • NM_001407368.1:c.1177G>A
  • NM_001407369.1:c.1177G>A
  • NM_001407370.1:c.1177G>A
  • NM_001407371.1:c.1177G>A
  • NM_001407372.1:c.1177G>A
  • NM_001407373.1:c.1177G>A
  • NM_001407374.1:c.1177G>A
  • NM_001407375.1:c.1177G>A
  • NM_001407376.1:c.1177G>A
  • NM_001407377.1:c.1177G>A
  • NM_001407378.1:c.1177G>A
  • NP_000051.1:p.Gly413Ser
  • NP_001268652.2:p.Gly393Ser
  • NP_001268652.2:p.Gly393Ser
  • NP_001268653.2:p.Gly393Ser
  • NP_001268654.1:p.Gly393Ser
  • NP_001268654.1:p.Gly393Ser
  • NP_001310511.1:p.Gly393Ser
  • NP_001310511.1:p.Gly393Ser
  • NP_001357587.1:p.Gly393Ser
  • NP_001394293.1:p.Gly393Ser
  • NP_001394294.1:p.Gly393Ser
  • NP_001394295.1:p.Gly393Ser
  • NP_001394296.1:p.Gly393Ser
  • NP_001394297.1:p.Gly393Ser
  • NP_001394298.1:p.Gly393Ser
  • NP_001394299.1:p.Gly393Ser
  • NP_001394300.1:p.Gly393Ser
  • NP_001394301.1:p.Gly393Ser
  • NP_001394302.1:p.Gly393Ser
  • NP_001394303.1:p.Gly393Ser
  • NP_001394304.1:p.Gly393Ser
  • NP_001394305.1:p.Gly393Ser
  • NP_001394306.1:p.Gly393Ser
  • NP_001394307.1:p.Gly393Ser
  • NC_000003.11:g.15686600G>A
  • NM_001281723.3:c.1177G>A
  • NM_001281725.2:c.1177G>A
  • NM_001323582.1:c.1177G>A
Protein change:
G393S
Links:
dbSNP: rs374141881
NCBI 1000 Genomes Browser:
rs374141881
Molecular consequence:
  • NM_001370752.1:c.1015+162G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001370753.1:c.399+3036G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000060.4:c.1237G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001281723.4:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001281724.3:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001281725.3:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001323582.2:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370658.1:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407364.1:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407365.1:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407366.1:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407367.1:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407368.1:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407369.1:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407370.1:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407371.1:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407372.1:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407373.1:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407374.1:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407375.1:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407376.1:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407377.1:c.1177G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407378.1:c.1177G>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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000630321Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Dec 5, 2023) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV000800639Counsyl
criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))		Uncertain significance
(Dec 14, 2017) 		unknownclinical testing

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

Citation Link,

SCV001461223Natera, Inc.
no assertion criteria provided
Uncertain significance
(Sep 16, 2020) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical 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

Outcomes of individuals with profound and partial biotinidase deficiency ascertained by newborn screening in Michigan over 25 years.

Jay AM, Conway RL, Feldman GL, Nahhas F, Spencer L, Wolf B.

Genet Med. 2015 Mar;17(3):205-9. doi: 10.1038/gim.2014.104. Epub 2014 Aug 21.

PubMed [citation]
PMID:
25144890

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000630321.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 413 of the BTD protein (p.Gly413Ser). This variant is present in population databases (rs374141881, gnomAD 0.003%). This missense change has been observed in individual(s) with partial biotinidase deficiency (PMID: 25144890). ClinVar contains an entry for this variant (Variation ID: 38577). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt BTD protein function with a positive predictive value of 95%. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Counsyl, SCV000800639.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV001461223.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 8, 2024