NM_001352514.2(HLCS):c.929del (p.Asn310fs) AND Holocarboxylase synthetase deficiency

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 26, 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:: RCV003468342.1

Allele description [Variation Report for NM_001352514.2(HLCS):c.929del (p.Asn310fs)]

NM_001352514.2(HLCS):c.929del (p.Asn310fs)

Gene:

HLCS:holocarboxylase synthetase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

21q22.13

Genomic location:

Preferred name:

NM_001352514.2(HLCS):c.929del (p.Asn310fs)

HGVS:

NC_000021.9:g.36936958del
NG_016193.2:g.58438del
NM_000411.8:c.488del
NM_001242784.3:c.488del
NM_001242785.2:c.488del
NM_001352514.2:c.929delMANE SELECT
NM_001352515.2:c.488del
NM_001352516.2:c.488del
NM_001352517.1:c.488del
NM_001352518.2:c.488del
NP_000402.3:p.Asn163fs
NP_001229713.1:p.Asn163fs
NP_001229714.1:p.Asn163fs
NP_001339443.1:p.Asn310fs
NP_001339444.1:p.Asn163fs
NP_001339445.1:p.Asn163fs
NP_001339446.1:p.Asn163fs
NP_001339447.1:p.Asn163fs
NC_000021.8:g.38309258del
NR_148020.2:n.788del
NR_148021.1:n.945del

Protein change:

N163fs

Molecular consequence:

NM_000411.8:c.488del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001242784.3:c.488del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001242785.2:c.488del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001352514.2:c.929del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001352515.2:c.488del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001352516.2:c.488del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001352517.1:c.488del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001352518.2:c.488del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_148020.2:n.788del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148021.1:n.945del - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004199844	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 26, 2023)	unknown	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

SCV004199844

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jun 26, 2023)

unknown

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Baylor Genetics, SCV004199844.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 30, 2023

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