NM_001370658.1(BTD):c.622G>T (p.Asp208Tyr) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Feb 18, 2021
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:: RCV000185805.17

Allele description [Variation Report for NM_001370658.1(BTD):c.622G>T (p.Asp208Tyr)]

NM_001370658.1(BTD):c.622G>T (p.Asp208Tyr)

Gene:

BTD:biotinidase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p25.1

Genomic location:

Preferred name:

NM_001370658.1(BTD):c.622G>T (p.Asp208Tyr)

Other names:

p.D228Y:GAT>TAT

HGVS:

NC_000003.12:g.15644538G>T
NG_008019.2:g.48187G>T
NG_008019.3:g.48188G>T
NM_000060.4:c.682G>T
NM_001281723.4:c.622G>T
NM_001281724.3:c.622G>T
NM_001281725.3:c.622G>T
NM_001323582.2:c.622G>T
NM_001370658.1:c.622G>TMANE SELECT
NM_001370752.1:c.622G>T
NM_001370753.1:c.399+2481G>T
NM_001407364.1:c.622G>T
NM_001407365.1:c.622G>T
NM_001407366.1:c.622G>T
NM_001407367.1:c.622G>T
NM_001407368.1:c.622G>T
NM_001407369.1:c.622G>T
NM_001407370.1:c.622G>T
NM_001407371.1:c.622G>T
NM_001407372.1:c.622G>T
NM_001407373.1:c.622G>T
NM_001407374.1:c.622G>T
NM_001407375.1:c.622G>T
NM_001407376.1:c.622G>T
NM_001407377.1:c.622G>T
NM_001407378.1:c.622G>T
NM_001407379.1:c.622G>T
NP_000051.1:p.Asp228Tyr
NP_001268652.2:p.Asp208Tyr
NP_001268652.2:p.Asp208Tyr
NP_001268653.2:p.Asp208Tyr
NP_001268654.1:p.Asp208Tyr
NP_001268654.1:p.Asp208Tyr
NP_001310511.1:p.Asp208Tyr
NP_001310511.1:p.Asp208Tyr
NP_001357587.1:p.Asp208Tyr
NP_001357681.1:p.Asp208Tyr
NP_001394293.1:p.Asp208Tyr
NP_001394294.1:p.Asp208Tyr
NP_001394295.1:p.Asp208Tyr
NP_001394296.1:p.Asp208Tyr
NP_001394297.1:p.Asp208Tyr
NP_001394298.1:p.Asp208Tyr
NP_001394299.1:p.Asp208Tyr
NP_001394300.1:p.Asp208Tyr
NP_001394301.1:p.Asp208Tyr
NP_001394302.1:p.Asp208Tyr
NP_001394303.1:p.Asp208Tyr
NP_001394304.1:p.Asp208Tyr
NP_001394305.1:p.Asp208Tyr
NP_001394306.1:p.Asp208Tyr
NP_001394307.1:p.Asp208Tyr
NP_001394308.1:p.Asp208Tyr
NC_000003.11:g.15686045G>T
NM_001281723.3:c.622G>T
NM_001281725.2:c.622G>T
NM_001323582.1:c.622G>T
P43251:p.Asp228Tyr

Protein change:

D208Y

Links:

UniProtKB: P43251#VAR_005115; dbSNP: rs397514380

NCBI 1000 Genomes Browser:

rs397514380

Molecular consequence:

NM_001370753.1:c.399+2481G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000060.4:c.682G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001281723.4:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001281724.3:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001281725.3:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001323582.2:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370658.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370752.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407364.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407365.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407366.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407367.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407368.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407369.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407370.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407371.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407372.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407373.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407374.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407375.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407376.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407377.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407378.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407379.1:c.622G>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000238747	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Jan 19, 2016)	germline	clinical testing	Citation Link,
SCV002046648	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely pathogenic (Feb 18, 2021)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 9654207, 11668630, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000238747

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Jan 19, 2016)

germline

clinical testing

Citation Link,

SCV002046648

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Likely pathogenic
(Feb 18, 2021)

unknown

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

Mutations in BTD causing biotinidase deficiency.

Hymes J, Stanley CM, Wolf B.

Hum Mutat. 2001 Nov;18(5):375-81. Review.

PubMed [citation]

PMID:: 11668630

See all PubMed Citations (3)

Details of each submission

From GeneDx, SCV000238747.11

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

Description

The D228Y missense mutation in the BTD gene has been reported previously in association with biotinidase deficiency (Swango et al., 1998; ARUP BTD mutation database). Furthermore, another missense mutation at this position (D228G) and missense mutations in nearby residues (D222G, T234I) have been reported in association with biotinidase deficiency.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Eurofins Ntd Llc (ga), SCV000855891.1

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

#	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		1	not provided	not provided	not provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002046648.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

The variant has been reported to be associated with partial biotinidase deficiency (PMID: 9654207 (1998)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is disease causing and damaging. Based on the available information, this variant is classified as likely pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000855891	Eurofins Ntd Llc (ga)	flagged submission Reason: Outlier claim with insufficient supporting evidence Notes: None (EGL Classification Definitions 2015)	Uncertain significance (Aug 2, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000855891

Eurofins Ntd Llc (ga)

flagged submission

Reason: Outlier claim with insufficient supporting evidence

Notes: None

(EGL Classification Definitions 2015)

Uncertain significance
(Aug 2, 2017)

germline

clinical testing

Citation Link

Last Updated: Nov 24, 2024

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