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NM_006895.3(HNMT):c.475del (p.His159fs) AND multiple conditions

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 10, 2022
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:
RCV003227774.1

Allele description [Variation Report for NM_006895.3(HNMT):c.475del (p.His159fs)]

NM_006895.3(HNMT):c.475del (p.His159fs)

Gene:
HNMT:histamine N-methyltransferase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2q22.1
Genomic location:
Preferred name:
NM_006895.3(HNMT):c.475del (p.His159fs)
HGVS:
  • NC_000002.12:g.138005177del
  • NG_012966.1:g.45940del
  • NM_006895.3:c.475delMANE SELECT
  • NP_008826.1:p.His159fs
  • NC_000002.11:g.138762747del
  • NM_006895.3:c.475delCMANE SELECT
Protein change:
H159fs
Links:
dbSNP: rs765863580
NCBI 1000 Genomes Browser:
rs765863580
Molecular consequence:
  • NM_006895.3:c.475del - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

Condition(s)

Name:
Inherited susceptibility to asthma
Synonyms:
ASTHMA, BRONCHIAL; ASTHMA-RELATED TRAITS, SUSCEPTIBILITY TO; Asthma, susceptibility to
Identifiers:
MONDO: MONDO:0010940; MedGen: C1869116; OMIM: 600807
Name:
Intellectual disability, autosomal recessive 51 (MRT51)
Synonyms:
INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 51
Identifiers:
MONDO: MONDO:0014759; MedGen: C4225220; Orphanet: 88616; OMIM: 616739

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003925170New York Genome Center
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Likely pathogenic
(Jun 10, 2022) 		inheritedclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedunknown1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center, SCV003925170.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The c.475del variant in HNMT has not previously been reported in the literature but it has been deposited in ClinVar [ClinVar ID: 445774] as Likely pathogenic. The c.475del variant is observed in 21 alleles (~0.00004% minor allele frequency with 0 homozygotes) in population databases (gnomAD v2.1.1 and v3.1.2, TOPMedFreeze 8. All of Us), suggesting it is not a common benign variant in the populations represented in those databases. The c.475del variant in HNMT is located in exon 5 of this 6-exon gene, and is predicted to incorporate a premature termination codon (p.(His159IlefsTer4), which might result in either loss-of-function via nonsense mediated decay or loss of the last 129 amino acids (>10% of the protein). Based on available evidence this inherited c.475del p.(His159IlefsTer4) variant identified in HNMT is classified as Likely Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

Last Updated: Jan 6, 2024