NM_015346.4(ZFYVE26):c.2826G>A (p.Met942Ile) AND not provided

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Aug 1, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000713429.21

Allele description [Variation Report for NM_015346.4(ZFYVE26):c.2826G>A (p.Met942Ile)]

NM_015346.4(ZFYVE26):c.2826G>A (p.Met942Ile)

Gene:

ZFYVE26:zinc finger FYVE-type containing 26 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q24.1

Genomic location:

Preferred name:

NM_015346.4(ZFYVE26):c.2826G>A (p.Met942Ile)

HGVS:

NC_000014.9:g.67789528C>T
NG_011836.1:g.32062G>A
NM_015346.4:c.2826G>AMANE SELECT
NP_056161.2:p.Met942Ile
NC_000014.8:g.68256245C>T
NM_015346.3:c.2826G>A

Protein change:

M942I

Links:

dbSNP: rs117367857

NCBI 1000 Genomes Browser:

rs117367857

Molecular consequence:

NM_015346.4:c.2826G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000844036	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Jan 16, 2018)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 19917823, 26467025
SCV002822143	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Aug 1, 2024)	germline	clinical testing	Citation Link,
SCV005212448	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000844036

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Benign
(Jan 16, 2018)

germline

clinical testing

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

SCV002822143

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Benign
(Aug 1, 2024)

germline

clinical testing

Citation Link,

SCV005212448

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign

germline

not provided

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	20	not provided	not provided	not provided	not provided	clinical testing, not provided
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Frequency and phenotype of SPG11 and SPG15 in complicated hereditary spastic paraplegia.

Schüle R, Schlipf N, Synofzik M, Klebe S, Klimpe S, Hehr U, Winner B, Lindig T, Dotzer A, Riess O, Winkler J, Schöls L, Bauer P.

J Neurol Neurosurg Psychiatry. 2009 Dec;80(12):1402-4. doi: 10.1136/jnnp.2008.167528.

PubMed [citation]

PMID:: 19917823

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

See all PubMed Citations (3)

Details of each submission

From Athena Diagnostics, SCV000844036.1

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

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV002822143.14

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	20	not provided	not provided	clinical testing	not provided

Description

ZFYVE26: BP4, BS1, BS2

#	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		20	not provided	not provided	not provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005212448.1

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

#	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: Oct 20, 2024

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