NM_001370298.3(FGD4):c.647C>T (p.Thr216Ile) AND not provided

Germline classification:: Likely benign (3 submissions)
Last evaluated:: Apr 26, 2021
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:: RCV000757290.9

Allele description [Variation Report for NM_001370298.3(FGD4):c.647C>T (p.Thr216Ile)]

NM_001370298.3(FGD4):c.647C>T (p.Thr216Ile)

Gene:

FGD4:FYVE, RhoGEF and PH domain containing 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12p11.21

Genomic location:

Preferred name:

NM_001370298.3(FGD4):c.647C>T (p.Thr216Ile)

HGVS:

NC_000012.12:g.32582103C>T
NG_008626.2:g.187575C>T
NM_001304481.2:c.491C>T
NM_001304483.2:c.-609C>T
NM_001304484.2:c.-916C>T
NM_001330373.2:c.-44C>T
NM_001330374.2:c.-44C>T
NM_001370297.1:c.49-16394C>T
NM_001370298.3:c.647C>TMANE SELECT
NM_001384126.1:c.647C>T
NM_001384127.1:c.236C>T
NM_001384128.1:c.236C>T
NM_001384130.1:c.-44C>T
NM_001384131.1:c.236C>T
NM_001384132.1:c.236C>T
NM_001385118.1:c.236C>T
NM_139241.3:c.236C>T
NP_001291410.1:p.Thr164Ile
NP_001291410.1:p.Thr164Ile
NP_001357227.2:p.Thr216Ile
NP_001371055.1:p.Thr216Ile
NP_001371056.1:p.Thr79Ile
NP_001371057.1:p.Thr79Ile
NP_001371060.1:p.Thr79Ile
NP_001371061.1:p.Thr79Ile
NP_001372047.1:p.Thr79Ile
NP_640334.2:p.Thr79Ile
LRG_240t1:c.236C>T
LRG_240t2:c.491C>T
LRG_240:g.187575C>T
LRG_240p1:p.Thr79Ile
LRG_240p2:p.Thr164Ile
NC_000012.11:g.32735037C>T
NM_001304481.1:c.491C>T
NM_139241.2:c.236C>T
NR_168884.1:n.473C>T

Protein change:

T164I

Links:

dbSNP: rs145115430

NCBI 1000 Genomes Browser:

rs145115430

Molecular consequence:

NM_001304483.2:c.-609C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001304484.2:c.-916C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001330373.2:c.-44C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001330374.2:c.-44C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001384130.1:c.-44C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370297.1:c.49-16394C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001304481.2:c.491C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370298.3:c.647C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001384126.1:c.647C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001384127.1:c.236C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001384128.1:c.236C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001384131.1:c.236C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001384132.1:c.236C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001385118.1:c.236C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_139241.3:c.236C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_168884.1:n.473C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV001143906	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Likely benign (Nov 9, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001771086	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Apr 26, 2021)	germline	clinical testing	Citation Link,
SCV005216561	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

SCV001143906

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Likely benign
(Nov 9, 2018)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001771086

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Apr 26, 2021)

germline

clinical testing

Citation Link,

SCV005216561

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	not provided	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

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

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 Athena Diagnostics, SCV001143906.1

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

#	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 GeneDx, SCV001771086.1

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

#	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

From Breakthrough Genomics, Breakthrough Genomics, SCV005216561.1

#	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 13, 2024

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