NM_000190.4(HMBS):c.962G>A (p.Arg321His) AND Acute intermittent porphyria

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Apr 27, 2017
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000148508.9

Allele description [Variation Report for NM_000190.4(HMBS):c.962G>A (p.Arg321His)]

NM_000190.4(HMBS):c.962G>A (p.Arg321His)

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.962G>A (p.Arg321His)

HGVS:

NC_000011.10:g.119093159G>A
NG_008093.1:g.13283G>A
NM_000190.4:c.962G>AMANE SELECT
NM_001024382.2:c.911G>A
NM_001258208.2:c.842G>A
NM_001258209.2:c.791G>A
NP_000181.2:p.Arg321His
NP_001019553.1:p.Arg304His
NP_001245137.1:p.Arg281His
NP_001245138.1:p.Arg264His
LRG_1076t1:c.962G>A
LRG_1076t2:c.911G>A
LRG_1076:g.13283G>A
LRG_1076p1:p.Arg321His
LRG_1076p2:p.Arg304His
NC_000011.9:g.118963869G>A
NM_000190.3:c.962G>A

Protein change:

R264H

Links:

dbSNP: rs150428209

NCBI 1000 Genomes Browser:

rs150428209

Molecular consequence:

NM_000190.4:c.962G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001024382.2:c.911G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001258208.2:c.842G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001258209.2:c.791G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Acute intermittent porphyria (AIP)
Synonyms:: Porphobilinogen deaminase deficiency; Uroporphyrinogen synthase deficiency; UPS deficiency; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008294; MedGen: C0162565; Orphanet: 79276; OMIM: 176000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000190219	CSER _CC_NCGL, University of Washington - ESP 6500 variant annotation	no assertion criteria provided	Likely benign (Jun 1, 2014)	germline	research
SCV000367707	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	Citation Link,
SCV001132051	Mount Sinai Diagnostic Laboratory, Icahn School of Medicine at Mount Sinai	criteria provided, single submitter (Chen et al. (Hum Mutat. 2016))	Benign	not applicable	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000190219

CSER _CC_NCGL, University of Washington - ESP 6500 variant annotation

no assertion criteria provided

Likely benign
(Jun 1, 2014)

germline

research

SCV000367707

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

Citation Link,

SCV001132051

Mount Sinai Diagnostic Laboratory, Icahn School of Medicine at Mount Sinai

criteria provided, single submitter

(Chen et al. (Hum Mutat. 2016))

Benign

not applicable

research

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing, research
not provided	not applicable	not applicable	not provided	not provided	not provided	not provided	not provided	research

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

Details of each submission

From CSER _CC_NCGL, University of Washington - ESP 6500 variant annotation, SCV000190219.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Illumina Laboratory Services, Illumina, SCV000367707.3

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mount Sinai Diagnostic Laboratory, Icahn School of Medicine at Mount Sinai, SCV001132051.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	not applicable	not applicable	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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