NM_022489.4(INF2):c.490_498del (p.Ala164_Asp166del) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 6, 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:: RCV000543208.7

Allele description [Variation Report for NM_022489.4(INF2):c.490_498del (p.Ala164_Asp166del)]

NM_022489.4(INF2):c.490_498del (p.Ala164_Asp166del)

Gene:

INF2:inverted formin 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

14q32.33

Genomic location:

Preferred name:

NM_022489.4(INF2):c.490_498del (p.Ala164_Asp166del)

HGVS:

NC_000014.9:g.104703203_104703211del
NG_027684.1:g.18598_18606del
NM_001031714.4:c.490_498del
NM_022489.4:c.490_498delMANE SELECT
NM_032714.3:c.490_498del
NP_001026884.3:p.Ala164_Asp166del
NP_071934.3:p.Ala164_Asp166del
NP_116103.1:p.Ala164_Asp166del
NC_000014.8:g.105169532_105169540del
NC_000014.8:g.105169540_105169548del
NM_022489.3:c.490_498delGCCCTGGAC

Links:

OMIM: 610982.0011; dbSNP: rs1555373599

NCBI 1000 Genomes Browser:

rs1555373599

Molecular consequence:

NM_001031714.4:c.490_498del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_022489.4:c.490_498del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_032714.3:c.490_498del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Focal segmental glomerulosclerosis 5 (FSGS5)
Identifiers:: MONDO: MONDO:0013191; MedGen: C2750475; Orphanet: 656; OMIM: 613237

Name:: Charcot-Marie-Tooth disease dominant intermediate E
Synonyms:: CHARCOT-MARIE-TOOTH NEUROPATHY WITH FOCAL SEGMENTAL GLOMERULONEPHRITIS
Identifiers:: MONDO: MONDO:0013758; MedGen: C4302667; Orphanet: 93114; OMIM: 614455

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000652132	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 6, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22187985, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000652132

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 6, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

INF2 mutations in Charcot-Marie-Tooth disease with glomerulopathy.

Boyer O, Nevo F, Plaisier E, Funalot B, Gribouval O, Benoit G, Huynh Cong E, Arrondel C, Tête MJ, Montjean R, Richard L, Karras A, Pouteil-Noble C, Balafrej L, Bonnardeaux A, Canaud G, Charasse C, Dantal J, Deschenes G, Deteix P, Dubourg O, Petiot P, et al.

N Engl J Med. 2011 Dec 22;365(25):2377-88. doi: 10.1056/NEJMoa1109122.

PubMed [citation]

PMID:: 22187985

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000652132.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant has been observed in individual(s) with Charcot-Marie-Tooth (CMT) and focal segmental glomerulosclerosis (PMID: 22187985; Invitae). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This variant, c.490_498del, results in the deletion of 3 amino acid(s) of the INF2 protein (p.Ala164_Asp166del), but otherwise preserves the integrity of the reading frame. ClinVar contains an entry for this variant (Variation ID: 472868). For these reasons, this variant has been 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: Mar 5, 2024

ClinVar

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