NM_022041.4(GAN):c.47_48delinsAC (p.Leu16His) AND Giant axonal neuropathy 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 15, 2023
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:: RCV001926096.6

Allele description [Variation Report for NM_022041.4(GAN):c.47_48delinsAC (p.Leu16His)]

NM_022041.4(GAN):c.47_48delinsAC (p.Leu16His)

Genes:

LOC130059498:ATAC-STARR-seq lymphoblastoid silent region 7753 [Gene]
GAN:gigaxonin [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

16q23.2

Genomic location:

Preferred name:

NM_022041.4(GAN):c.47_48delinsAC (p.Leu16His)

HGVS:

NC_000016.10:g.81315160_81315161delinsAC
NG_009007.1:g.5195_5196delinsAC
NM_001377486.1:c.-478_-477delinsAC
NM_022041.4:c.47_48delinsACMANE SELECT
NP_071324.1:p.Leu16His
LRG_242:g.5195_5196delinsAC
NC_000016.9:g.81348765_81348766delinsAC

Protein change:

L16H

Links:

dbSNP: rs2150663586

NCBI 1000 Genomes Browser:

rs2150663586

Molecular consequence:

NM_001377486.1:c.-478_-477delinsAC - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_022041.4:c.47_48delinsAC - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Giant axonal neuropathy 1 (GAN1)
Synonyms:: GIANT AXONAL NEUROPATHY 1, AUTOSOMAL RECESSIVE
Identifiers:: MONDO: MONDO:0009749; MedGen: C1850386; Orphanet: 643; OMIM: 256850

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002187753	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 15, 2023)	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

SCV002187753

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 15, 2023)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002187753.3

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

Description

Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 1422264). This variant has not been reported in the literature in individuals affected with GAN-related conditions. This sequence change replaces leucine, which is neutral and non-polar, with histidine, which is basic and polar, at codon 16 of the GAN protein (p.Leu16His).

#	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: Sep 29, 2024

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