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NM_000190.4(HMBS):c.688G>T (p.Asp230Tyr) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 14, 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:
RCV003062465.3

Allele description [Variation Report for NM_000190.4(HMBS):c.688G>T (p.Asp230Tyr)]

NM_000190.4(HMBS):c.688G>T (p.Asp230Tyr)

Gene:
HMBS:hydroxymethylbilane synthase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q23.3
Genomic location:
Preferred name:
NM_000190.4(HMBS):c.688G>T (p.Asp230Tyr)
HGVS:
  • NC_000011.10:g.119092440G>T
  • NG_008093.1:g.12564G>T
  • NM_000190.4:c.688G>TMANE SELECT
  • NM_001024382.2:c.637G>T
  • NM_001258208.2:c.651+277G>T
  • NM_001258209.2:c.600+277G>T
  • NP_000181.2:p.Asp230Tyr
  • NP_001019553.1:p.Asp213Tyr
  • LRG_1076t1:c.688G>T
  • LRG_1076t2:c.637G>T
  • LRG_1076:g.12564G>T
  • LRG_1076p1:p.Asp230Tyr
  • LRG_1076p2:p.Asp213Tyr
  • NC_000011.9:g.118963150G>T
Protein change:
D213Y
Molecular consequence:
  • NM_001258208.2:c.651+277G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001258209.2:c.600+277G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000190.4:c.688G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001024382.2:c.637G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV003441180Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Jan 14, 2023)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Acute Intermittent Porphyria: Predicted Pathogenicity of HMBS Variants Indicates Extremely Low Penetrance of the Autosomal Dominant Disease.

Chen B, Solis-Villa C, Hakenberg J, Qiao W, Srinivasan RR, Yasuda M, Balwani M, Doheny D, Peter I, Chen R, Desnick RJ.

Hum Mutat. 2016 Nov;37(11):1215-1222. doi: 10.1002/humu.23067. Epub 2016 Sep 5.

PubMed [citation]
PMID:
27539938
PMCID:
PMC5063710

Diagnostic strategies for autosomal dominant acute porphyrias: retrospective analysis of 467 unrelated patients referred for mutational analysis of the HMBS, CPOX, or PPOX gene.

Whatley SD, Mason NG, Woolf JR, Newcombe RG, Elder GH, Badminton MN.

Clin Chem. 2009 Jul;55(7):1406-14. doi: 10.1373/clinchem.2008.122564. Epub 2009 May 21.

PubMed [citation]
PMID:
19460837
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003441180.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on HMBS function (PMID: 27539938). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt HMBS protein function. This missense change has been observed in individual(s) with clinical features of acute intermittent porphyria (PMID: 19460837). This variant is present in population databases (rs746221527, gnomAD 0.002%). This sequence change replaces aspartic acid, which is acidic and polar, with tyrosine, which is neutral and polar, at codon 230 of the HMBS protein (p.Asp230Tyr).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024