NM_001352514.2(HLCS):c.737A>G (p.Tyr246Cys) AND Holocarboxylase synthetase deficiency

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Aug 21, 2023
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:: RCV001277488.4

Allele description [Variation Report for NM_001352514.2(HLCS):c.737A>G (p.Tyr246Cys)]

NM_001352514.2(HLCS):c.737A>G (p.Tyr246Cys)

Gene:

HLCS:holocarboxylase synthetase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

21q22.13

Genomic location:

Preferred name:

NM_001352514.2(HLCS):c.737A>G (p.Tyr246Cys)

HGVS:

NC_000021.9:g.36937149T>C
NG_016193.2:g.58246A>G
NM_000411.8:c.296A>G
NM_001242784.3:c.296A>G
NM_001242785.2:c.296A>G
NM_001352514.2:c.737A>GMANE SELECT
NM_001352515.2:c.296A>G
NM_001352516.2:c.296A>G
NM_001352517.1:c.296A>G
NM_001352518.2:c.296A>G
NP_000402.3:p.Tyr99Cys
NP_001229713.1:p.Tyr99Cys
NP_001229714.1:p.Tyr99Cys
NP_001339443.1:p.Tyr246Cys
NP_001339444.1:p.Tyr99Cys
NP_001339445.1:p.Tyr99Cys
NP_001339446.1:p.Tyr99Cys
NP_001339447.1:p.Tyr99Cys
NC_000021.8:g.38309449T>C
NR_148020.2:n.596A>G
NR_148021.1:n.753A>G

Protein change:

Y246C

Links:

dbSNP: rs765150200

NCBI 1000 Genomes Browser:

rs765150200

Molecular consequence:

NM_000411.8:c.296A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001242784.3:c.296A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001242785.2:c.296A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001352514.2:c.737A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001352515.2:c.296A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001352516.2:c.296A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001352517.1:c.296A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001352518.2:c.296A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_148020.2:n.596A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148021.1:n.753A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Holocarboxylase synthetase deficiency
Synonyms:: MULTIPLE CARBOXYLASE DEFICIENCY, EARLY ONSET
Identifiers:: MONDO: MONDO:0009666; MedGen: C0268581; Orphanet: 79242; OMIM: 253270

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001464443	Natera, Inc.	no assertion criteria provided	Uncertain significance (Sep 4, 2020)	germline	clinical testing
SCV002947698	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Aug 21, 2023)	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

SCV001464443

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Sep 4, 2020)

germline

clinical testing

SCV002947698

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Aug 21, 2023)

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 Natera, Inc., SCV001464443.1

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002947698.2

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

#	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

ClinVar

Relating variation to medicine