NM_001352514.2(HLCS):c.569_585delinsTTGCTTGAGATTAAGCCTGAGATTAAGG (p.Pro190_Ser195delinsLeuAlaTer) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 23, 2016
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:: RCV000479512.1

Allele description [Variation Report for NM_001352514.2(HLCS):c.569_585delinsTTGCTTGAGATTAAGCCTGAGATTAAGG (p.Pro190_Ser195delinsLeuAlaTer)]

NM_001352514.2(HLCS):c.569_585delinsTTGCTTGAGATTAAGCCTGAGATTAAGG (p.Pro190_Ser195delinsLeuAlaTer)

Gene:

HLCS:holocarboxylase synthetase [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

21q22.13

Genomic location:

Preferred name:

NM_001352514.2(HLCS):c.569_585delinsTTGCTTGAGATTAAGCCTGAGATTAAGG (p.Pro190_Ser195delinsLeuAlaTer)

HGVS:

NC_000021.9:g.36937301_36937317delinsCCTTAATCTCAGGCTTAATCTCAAGCAA
NG_016193.2:g.58078_58094delinsTTGCTTGAGATTAAGCCTGAGATTAAGG
NM_000411.8:c.128_144delinsTTGCTTGAGATTAAGCCTGAGATTAAGG
NM_001242784.3:c.128_144delinsTTGCTTGAGATTAAGCCTGAGATTAAGG
NM_001242785.2:c.128_144delinsTTGCTTGAGATTAAGCCTGAGATTAAGG
NM_001352514.2:c.569_585delinsTTGCTTGAGATTAAGCCTGAGATTAAGGMANE SELECT
NM_001352515.2:c.128_144delinsTTGCTTGAGATTAAGCCTGAGATTAAGG
NM_001352516.2:c.128_144delinsTTGCTTGAGATTAAGCCTGAGATTAAGG
NM_001352517.1:c.128_144delinsTTGCTTGAGATTAAGCCTGAGATTAAGG
NM_001352518.2:c.128_144delinsTTGCTTGAGATTAAGCCTGAGATTAAGG
NP_000402.3:p.Pro43_Ser48delinsLeuAlaTer
NP_001229713.1:p.Pro43_Ser48delinsLeuAlaTer
NP_001229714.1:p.Pro43_Ser48delinsLeuAlaTer
NP_001339443.1:p.Pro190_Ser195delinsLeuAlaTer
NP_001339444.1:p.Pro43_Ser48delinsLeuAlaTer
NP_001339445.1:p.Pro43_Ser48delinsLeuAlaTer
NP_001339446.1:p.Pro43_Ser48delinsLeuAlaTer
NP_001339447.1:p.Pro43_Ser48delinsLeuAlaTer
NC_000021.8:g.38309601_38309617delinsCCTTAATCTCAGGCTTAATCTCAAGCAA
NM_000411.6:c.128_144delinsTTGCTTGAGATTAAGCCTGAGATTAAGG
NR_148020.2:n.428_444delinsTTGCTTGAGATTAAGCCTGAGATTAAGG
NR_148021.1:n.585_601delinsTTGCTTGAGATTAAGCCTGAGATTAAGG

Links:

dbSNP: rs1064796014

NCBI 1000 Genomes Browser:

rs1064796014

Molecular consequence:

NR_148020.2:n.428_444delinsTTGCTTGAGATTAAGCCTGAGATTAAGG - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148021.1:n.585_601delinsTTGCTTGAGATTAAGCCTGAGATTAAGG - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000411.8:c.128_144delinsTTGCTTGAGATTAAGCCTGAGATTAAGG - nonsense - [Sequence Ontology: SO:0001587]
NM_001242784.3:c.128_144delinsTTGCTTGAGATTAAGCCTGAGATTAAGG - nonsense - [Sequence Ontology: SO:0001587]
NM_001242785.2:c.128_144delinsTTGCTTGAGATTAAGCCTGAGATTAAGG - nonsense - [Sequence Ontology: SO:0001587]
NM_001352514.2:c.569_585delinsTTGCTTGAGATTAAGCCTGAGATTAAGG - nonsense - [Sequence Ontology: SO:0001587]
NM_001352515.2:c.128_144delinsTTGCTTGAGATTAAGCCTGAGATTAAGG - nonsense - [Sequence Ontology: SO:0001587]
NM_001352516.2:c.128_144delinsTTGCTTGAGATTAAGCCTGAGATTAAGG - nonsense - [Sequence Ontology: SO:0001587]
NM_001352517.1:c.128_144delinsTTGCTTGAGATTAAGCCTGAGATTAAGG - nonsense - [Sequence Ontology: SO:0001587]
NM_001352518.2:c.128_144delinsTTGCTTGAGATTAAGCCTGAGATTAAGG - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000572377	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Nov 23, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000572377

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Nov 23, 2016)

germline

clinical testing

Citation Link

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

Details of each submission

From GeneDx, SCV000572377.3

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

Description

The c.128_144del17ins28 variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.128_144del17ins28 variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The c.128_144del17ins28 variant causes a frameshift starting with codon Proline 43, changes this amino acid to a Leucine residue and creates a premature Stop codon at position 3 of the new reading frame, denoted p.Pro43LeufsX3. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. In summary, we interpret this variant to be likely pathogenic.

#	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

Last Updated: Feb 7, 2023

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