NM_001352514.2(HLCS):c.1045del (p.Glu349fs) AND Holocarboxylase synthetase deficiency

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 30, 2021
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:: RCV002310383.2

Allele description [Variation Report for NM_001352514.2(HLCS):c.1045del (p.Glu349fs)]

NM_001352514.2(HLCS):c.1045del (p.Glu349fs)

Gene:

HLCS:holocarboxylase synthetase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

21q22.13

Genomic location:

Preferred name:

NM_001352514.2(HLCS):c.1045del (p.Glu349fs)

HGVS:

NC_000021.9:g.36936842del
NG_016193.2:g.58554del
NM_000411.8:c.604del
NM_001242784.3:c.604del
NM_001242785.2:c.604del
NM_001352514.2:c.1045delMANE SELECT
NM_001352515.2:c.604del
NM_001352516.2:c.604del
NM_001352517.1:c.604del
NM_001352518.2:c.604del
NP_000402.3:p.Glu202fs
NP_001229713.1:p.Glu202fs
NP_001229714.1:p.Glu202fs
NP_001339443.1:p.Glu349fs
NP_001339444.1:p.Glu202fs
NP_001339445.1:p.Glu202fs
NP_001339446.1:p.Glu202fs
NP_001339447.1:p.Glu202fs
NC_000021.8:g.38309142del
NR_148020.2:n.904del
NR_148021.1:n.1061del

Protein change:

E202fs

Molecular consequence:

NM_000411.8:c.604del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001242784.3:c.604del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001242785.2:c.604del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001352514.2:c.1045del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001352515.2:c.604del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001352516.2:c.604del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001352517.1:c.604del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001352518.2:c.604del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_148020.2:n.904del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148021.1:n.1061del - 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
SCV002602368	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))	Likely pathogenic (Dec 30, 2021)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002602368

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))

Likely pathogenic
(Dec 30, 2021)

unknown

clinical testing

Citation Link

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

Details of each submission

From Myriad Genetics, Inc., SCV002602368.2

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

Description

NM_000411.6(HLCS):c.604delG(E202Rfs*56) is expected to be pathogenic in the context of holocarboxylase synthetase deficiency. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in HLCS, a gene where loss-of-function variants are known to be pathogenic. Please note: this variant was assessed in the context of healthy population screening.

#	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 24, 2022

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