Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_001352514.2(HLCS):c.1550C>T (p.Thr517Ile)

Help
Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Dec 28, 2020)
Last evaluated:
May 17, 2019
Accession:
VCV000459943.4
Variation ID:
459943
Description:
single nucleotide variant
Help

NM_001352514.2(HLCS):c.1550C>T (p.Thr517Ile)

Allele ID
471639
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
21q22.13
Genomic location
21: 36930321 (GRCh38) GRCh38 UCSC
21: 38302621 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_000411.8:c.1109C>T NP_000402.3:p.Thr370Ile missense
NC_000021.8:g.38302621G>A
NC_000021.9:g.36930321G>A
... more HGVS
Protein change
T370I, T517I
Other names
-
Canonical SPDI
NC_000021.9:36930320:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00010
Trans-Omics for Precision Medicine (TOPMed) 0.00012
Exome Aggregation Consortium (ExAC) 0.00020
Links
ClinGen: CA10020529
dbSNP: rs575286749
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 4 criteria provided, multiple submitters, no conflicts May 17, 2019 RCV000558830.5
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
HLCS - - GRCh38
GRCh37
512 578

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Holocarboxylase synthetase deficiency
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000896809.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Uncertain significance
(May 17, 2019)
criteria provided, single submitter
Method: clinical testing
Holocarboxylase synthetase deficiency
Allele origin: germline
Invitae
Accession: SCV000631921.2
Submitted: (Feb 06, 2020)
Evidence details
Comment:
This sequence change replaces threonine with isoleucine at codon 370 of the HLCS protein (p.Thr370Ile). The threonine residue is weakly conserved and there is a … (more)
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Holocarboxylase synthetase deficiency
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001299309.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Jan 24, 2020)
no assertion criteria provided
Method: clinical testing
Holocarboxylase synthetase deficiency
Allele origin: germline
Natera, Inc.
Accession: SCV001455959.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

Help
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

Help
Title Author Journal Year Link
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 Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868

Text-mined citations for rs575286749...

Help
These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 24, 2021