NM_138694.4(PKHD1):c.2194G>T (p.Val732Phe) AND not provided

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: May 16, 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:: RCV000405708.31

Allele description [Variation Report for NM_138694.4(PKHD1):c.2194G>T (p.Val732Phe)]

NM_138694.4(PKHD1):c.2194G>T (p.Val732Phe)

Gene:

PKHD1:PKHD1 ciliary IPT domain containing fibrocystin/polyductin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6p12.2

Genomic location:

Preferred name:

NM_138694.4(PKHD1):c.2194G>T (p.Val732Phe)

HGVS:

NC_000006.12:g.52050242C>A
NG_008753.1:g.42384G>T
NM_138694.4:c.2194G>TMANE SELECT
NM_170724.3:c.2194G>T
NP_619639.3:p.Val732Phe
NP_733842.2:p.Val732Phe
NC_000006.11:g.51915040C>A
NM_138694.3:c.2194G>T
NM_170724.3:c.2194G>T
P08F94:p.Val732Phe

Protein change:

V732F

Links:

UniProtKB: P08F94#VAR_018534; dbSNP: rs201432731

NCBI 1000 Genomes Browser:

rs201432731

Molecular consequence:

NM_138694.4:c.2194G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_170724.3:c.2194G>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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glial cell line-derived neurotrophic factor isoform 2 precursor [Mus musculus]
glial cell line-derived neurotrophic factor isoform 2 precursor [Mus musculus]
gi|672349281|ref|NP_001288261.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000342912	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (Jun 9, 2016)	germline	clinical testing	Citation Link,
SCV001154775	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Jan 1, 2017)	germline	clinical testing	Citation Link,
SCV002032588	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (May 16, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000342912

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Uncertain significance
(Jun 9, 2016)

germline

clinical testing

Citation Link,

SCV001154775

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

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

Uncertain significance
(Jan 1, 2017)

germline

clinical testing

Citation Link,

SCV002032588

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(May 16, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	2	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000342912.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	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	unknown	not provided	not provided	not provided		2	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV001154775.27

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	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		2	not provided	not provided	not provided

From GeneDx, SCV002032588.4

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

Description

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic in patients with PKHD1-related disease to our knowledge; This variant is associated with the following publications: (PMID: 12874454)

#	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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