NM_198066.4(GNPNAT1):c.226G>A (p.Glu76Lys) AND Rhizomelic dysplasia, Ain-Naz type

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 29, 2021
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV001733892.1

Allele description [Variation Report for NM_198066.4(GNPNAT1):c.226G>A (p.Glu76Lys)]

NM_198066.4(GNPNAT1):c.226G>A (p.Glu76Lys)

Gene:

GNPNAT1:glucosamine-phosphate N-acetyltransferase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q22.1

Genomic location:

Preferred name:

NM_198066.4(GNPNAT1):c.226G>A (p.Glu76Lys)

Other names:

E76K

HGVS:

NC_000014.9:g.52781903C>T
NM_198066.4:c.226G>AMANE SELECT
NP_932332.1:p.Glu76Lys
NC_000014.8:g.53248621C>T

Protein change:

GLU76LYS

Links:

OMIM: 616510.0001; dbSNP: rs2139964469

NCBI 1000 Genomes Browser:

rs2139964469

Molecular consequence:

NM_198066.4:c.226G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Rhizomelic dysplasia, Ain-Naz type
Identifiers:: MONDO: MONDO:0859203; MedGen: C5562013; OMIM: 619598

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001985070	OMIM	no assertion criteria provided	Pathogenic (Oct 29, 2021)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001985070

OMIM

no assertion criteria provided

Pathogenic
(Oct 29, 2021)

germline

literature only

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	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Novel form of rhizomelic skeletal dysplasia associated with a homozygous variant in GNPNAT1.

Ain NU, Baroncelli M, Costantini A, Ishaq T, Taylan F, Nilsson O, Mäkitie O, Naz S.

J Med Genet. 2021 May;58(5):351-356. doi: 10.1136/jmedgenet-2020-106929. Epub 2020 Jun 26.

PubMed [citation]

PMID:: 32591345

Details of each submission

From OMIM, SCV001985070.1

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

Description

In 4 affected sibs from a consanguineous Pakistani family (NAD-07) with the Ain-Naz type of rhizomelic dysplasia (RHZDAN; 619598), Ain et al. (2021) identified homozygosity for a c.226G-A transition in the GNPNAT1 gene, resulting in a glu76-to-lys (E76K) substitution. The unaffected mother was heterozygous for the variant, which was not present in an unaffected niece, offspring of a deceased unaffected sib. The father was deceased and not tested. The mutation, which was confirmed by Sanger sequencing, was not found in 380 ethnically matched controls or in the 1000 Genomes Project and gnomAD databases.

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

Last Updated: Dec 24, 2023

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