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NM_001370658.1(BTD):c.908A>G (p.His303Arg) AND Biotinidase deficiency

Germline classification:
Conflicting interpretations of pathogenicity (5 submissions)
Last evaluated:
Jan 5, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV000021978.23

Allele description [Variation Report for NM_001370658.1(BTD):c.908A>G (p.His303Arg)]

NM_001370658.1(BTD):c.908A>G (p.His303Arg)

Gene:
BTD:biotinidase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p25.1
Genomic location:
Preferred name:
NM_001370658.1(BTD):c.908A>G (p.His303Arg)
Other names:
H323R
HGVS:
  • NC_000003.12:g.15644824A>G
  • NG_008019.2:g.48473A>G
  • NG_008019.3:g.48474A>G
  • NM_000060.4:c.968A>G
  • NM_001281723.4:c.908A>G
  • NM_001281724.3:c.908A>G
  • NM_001281725.3:c.908A>G
  • NM_001323582.2:c.908A>G
  • NM_001370658.1:c.908A>GMANE SELECT
  • NM_001370752.1:c.908A>G
  • NM_001370753.1:c.399+2767A>G
  • NM_001407364.1:c.908A>G
  • NM_001407365.1:c.908A>G
  • NM_001407366.1:c.908A>G
  • NM_001407367.1:c.908A>G
  • NM_001407368.1:c.908A>G
  • NM_001407369.1:c.908A>G
  • NM_001407370.1:c.908A>G
  • NM_001407371.1:c.908A>G
  • NM_001407372.1:c.908A>G
  • NM_001407373.1:c.908A>G
  • NM_001407374.1:c.908A>G
  • NM_001407375.1:c.908A>G
  • NM_001407376.1:c.908A>G
  • NM_001407377.1:c.908A>G
  • NM_001407378.1:c.908A>G
  • NM_001407379.1:c.908A>G
  • NP_000051.1:p.His323Arg
  • NP_000051.1:p.His323Arg
  • NP_001268652.2:p.His303Arg
  • NP_001268652.2:p.His303Arg
  • NP_001268653.2:p.His303Arg
  • NP_001268654.1:p.His303Arg
  • NP_001268654.1:p.His303Arg
  • NP_001310511.1:p.His303Arg
  • NP_001310511.1:p.His303Arg
  • NP_001357587.1:p.His303Arg
  • NP_001357681.1:p.His303Arg
  • NP_001394293.1:p.His303Arg
  • NP_001394294.1:p.His303Arg
  • NP_001394295.1:p.His303Arg
  • NP_001394296.1:p.His303Arg
  • NP_001394297.1:p.His303Arg
  • NP_001394298.1:p.His303Arg
  • NP_001394299.1:p.His303Arg
  • NP_001394300.1:p.His303Arg
  • NP_001394301.1:p.His303Arg
  • NP_001394302.1:p.His303Arg
  • NP_001394303.1:p.His303Arg
  • NP_001394304.1:p.His303Arg
  • NP_001394305.1:p.His303Arg
  • NP_001394306.1:p.His303Arg
  • NP_001394307.1:p.His303Arg
  • NP_001394308.1:p.His303Arg
  • NC_000003.11:g.15686331A>G
  • NG_008019.1:g.48077A>G
  • NM_000060.2:c.968A>G
  • NM_000060.3:c.968A>G
  • NM_001281723.3:c.908A>G
  • NM_001281723.3:c.908A>G
  • NM_001281725.2:c.908A>G
  • NM_001323582.1:c.908A>G
  • NM_001370658.1:c.908A>G
  • NP_000051.1:p.His323Pro
  • P43251:p.His323Arg
Protein change:
H303R
Links:
UniProtKB: P43251#VAR_005116; dbSNP: rs397507176
NCBI 1000 Genomes Browser:
rs397507176
Molecular consequence:
  • NM_001370753.1:c.399+2767A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000060.4:c.968A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001281723.4:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001281724.3:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001281725.3:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001323582.2:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370658.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370752.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407364.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407365.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407366.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407367.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407368.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407369.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407370.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407371.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407372.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407373.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407374.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407375.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407376.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407377.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407378.1:c.908A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001407379.1:c.908A>G - 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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000630341Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Oct 17, 2022)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV001136346Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2017)
Uncertain significance
(May 28, 2019)
unknownclinical testing

Citation Link,

SCV001454451Natera, Inc.
no assertion criteria provided
Uncertain significance
(Sep 25, 2017)
germlineclinical testing

SCV001522810Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 31, 2022)
unknownclinical testing

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

SCV004234890Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Jan 5, 2024)
germlineclinical testing

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

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

Biotinidase deficiency: Spectrum of molecular, enzymatic and clinical information from newborn screening Ontario, Canada (2007-2014).

Gannavarapu S, Prasad C, DiRaimo J, Napier M, Goobie S, Potter M, Chakraborty P, Karaceper M, Munoz T, Schulze A, MacKenzie J, Li L, Geraghty MT, Al-Dirbashi OY, Rupar CA.

Mol Genet Metab. 2015 Nov;116(3):146-51. doi: 10.1016/j.ymgme.2015.08.010. Epub 2015 Aug 31.

PubMed [citation]
PMID:
26361991

Partial biotinidase deficiency is usually due to the D444H mutation in the biotinidase gene.

Swango KL, Demirkol M, Hüner G, Pronicka E, Sykut-Cegielska J, Schulze A, Mayatepek E, Wolf B.

Hum Genet. 1998 May;102(5):571-5. Erratum in: Hum Genet 1998 Jun;102(6):712.

PubMed [citation]
PMID:
9654207
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV000630341.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change replaces histidine, which is basic and polar, with arginine, which is basic and polar, at codon 323 of the BTD protein (p.His323Arg). This variant is present in population databases (rs397507176, gnomAD 1.7%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individuals with partial BTD deficiency who showed 10-30% of normal BTD enzymatic activity (PMID: 9654207, 26361991). ClinVar contains an entry for this variant (Variation ID: 38278). 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. Experimental studies have shown that this missense change affects BTD function (PMID: 9654207, 24797656). 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 Mendelics, SCV001136346.1

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

From Natera, Inc., SCV001454451.1

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

From Baylor Genetics, SCV001522810.2

#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 Revvity Omics, Revvity, SCV004234890.1

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

Last Updated: May 26, 2024