NM_001371928.1(AHDC1):c.2188G>T (p.Glu730Ter) AND Inborn genetic diseases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 30, 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:: RCV002541580.2

Allele description [Variation Report for NM_001371928.1(AHDC1):c.2188G>T (p.Glu730Ter)]

NM_001371928.1(AHDC1):c.2188G>T (p.Glu730Ter)

Gene:

AHDC1:AT-hook DNA binding motif containing 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.11

Genomic location:

Preferred name:

NM_001371928.1(AHDC1):c.2188G>T (p.Glu730Ter)

HGVS:

NC_000001.11:g.27549928C>A
NG_034158.1:g.58567G>T
NM_001029882.3:c.2188G>T
NM_001371928.1:c.2188G>TMANE SELECT
NP_001025053.1:p.Glu730Ter
NP_001358857.1:p.Glu730Ter
NC_000001.10:g.27876439C>A
NM_001029882.2:c.2188G>T

Protein change:

E730*

Links:

dbSNP: rs2019433712

NCBI 1000 Genomes Browser:

rs2019433712

Molecular consequence:

NM_001029882.3:c.2188G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001371928.1:c.2188G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003647223	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Nov 30, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 28135719, 33644933, 35716097 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003647223

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Nov 30, 2022)

germline

clinical testing

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

Citation Link

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

Citations

PubMed

Prevalence and architecture of de novo mutations in developmental disorders.

Deciphering Developmental Disorders Study..

Nature. 2017 Feb 23;542(7642):433-438. doi: 10.1038/nature21062. Epub 2017 Jan 25.

PubMed [citation]

PMID:: 28135719
PMCID:: PMC6016744

Phenotypic and protein localization heterogeneity associated with AHDC1 pathogenic protein-truncating alleles in Xia-Gibbs syndrome.

Khayat MM, Li H, Chander V, Hu J, Hansen AW, Li S, Traynelis J, Shen H, Weissenberger G, Stossi F, Johnson HL, Lupski JR, Posey JE, Sabo A, Meng Q, Murdock DR, Wangler M, Gibbs RA.

Hum Mutat. 2021 May;42(5):577-591. doi: 10.1002/humu.24190. Epub 2021 Mar 6.

PubMed [citation]

PMID:: 33644933
PMCID:: PMC8115934

See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV003647223.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

The c.2188G>T (p.E730*) alteration, located in exon 6 (coding exon 1) of the AHDC1 gene, consists of a G to T substitution at nucleotide position 2188. This changes the amino acid from a glutamic acid (E) to a stop codon at amino acid position 730. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been reported de novo in multiple individuals with features consistent with Xia-Gibbs syndrome or an unspecified developmental disorder (Deciphering Developmental Disorders, 2017; Khayat, 2021; Romano, 2022). Based on the available evidence, this alteration is classified as pathogenic.

#	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

Last Updated: May 1, 2024

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