NM_001282531.3(ADNP):c.3110A>C (p.Glu1037Ala) AND ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder - ClinVar

NM_001282531.3(ADNP):c.3110A>C (p.Glu1037Ala) AND ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 2, 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:: RCV002470236.1

Allele description [Variation Report for NM_001282531.3(ADNP):c.3110A>C (p.Glu1037Ala)]

NM_001282531.3(ADNP):c.3110A>C (p.Glu1037Ala)

Gene:

ADNP:activity dependent neuroprotector homeobox [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

20q13.13

Genomic location:

Preferred name:

NM_001282531.3(ADNP):c.3110A>C (p.Glu1037Ala)

HGVS:

NC_000020.11:g.50891604T>G
NG_034200.1:g.44387A>C
NG_034200.2:g.44833A>C
NM_001282531.3:c.3110A>CMANE SELECT
NM_001282532.2:c.3110A>C
NM_001347511.2:c.3110A>C
NM_015339.5:c.3110A>C
NM_181442.4:c.3110A>C
NP_001269460.1:p.Glu1037Ala
NP_001269461.1:p.Glu1037Ala
NP_001334440.1:p.Glu1037Ala
NP_056154.1:p.Glu1037Ala
NP_852107.1:p.Glu1037Ala
NC_000020.10:g.49508141T>G
NM_001282531.2:c.3110A>C

Protein change:

E1037A

Molecular consequence:

NM_001282531.3:c.3110A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282532.2:c.3110A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001347511.2:c.3110A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_015339.5:c.3110A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_181442.4:c.3110A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: ADNP-related multiple congenital anomalies - intellectual disability - autism spectrum disorder
Synonyms:: ADNP-Related Disorders; Helsmoortel-Van der Aa Syndrome
Identifiers:: MONDO: MONDO:0014379; MedGen: C4014538; Orphanet: 404448; OMIM: 615873

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002766945	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 2, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002766945

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 2, 2022)

germline

clinical testing

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002766945.1

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

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3B. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Helsmoortel-van der Aa syndrome (MIM#615873). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from glutamic acid to alanine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (1 heterozygote, 0 homozygotes). (SP) 0501 - Missense variant consistently predicted to be benign by multiple in silico tools, but highly conserved with a major amino acid change. (SP) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0807 - This variant has no previous evidence of pathogenicity. (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

Last Updated: Dec 24, 2022

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