NM_138694.4(PKHD1):c.6245C>T (p.Thr2082Ile) AND not provided

Germline classification:: Benign (3 submissions)
Last evaluated:: Jul 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:: RCV000857781.11

Allele description [Variation Report for NM_138694.4(PKHD1):c.6245C>T (p.Thr2082Ile)]

NM_138694.4(PKHD1):c.6245C>T (p.Thr2082Ile)

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.6245C>T (p.Thr2082Ile)

HGVS:

NC_000006.12:g.51912453G>A
NG_008753.1:g.180173C>T
NM_138694.4:c.6245C>TMANE SELECT
NM_170724.3:c.6245C>T
NP_619639.3:p.Thr2082Ile
NP_733842.2:p.Thr2082Ile
NC_000006.11:g.51777251G>A
NM_138694.3:c.6245C>T

Protein change:

T2082I

Links:

dbSNP: rs147487242

NCBI 1000 Genomes Browser:

rs147487242

Molecular consequence:

NM_138694.4:c.6245C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_170724.3:c.6245C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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CYP405A2, partial [Zygaena transalpina]
CYP405A2, partial [Zygaena transalpina]
gi|1420818154|gb|AXB26339.1|

Protein
LOC124252626 [Homo sapiens]
LOC124252626 [Homo sapiens]
Gene ID:124252626

Gene
LOC129929032 [Homo sapiens]
LOC129929032 [Homo sapiens]
Gene ID:129929032

Gene
LOC126860599 [Homo sapiens]
LOC126860599 [Homo sapiens]
Gene ID:126860599

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001154772	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Jul 1, 2024)	germline	clinical testing	Citation Link,
SCV001936704	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Jul 5, 2018)	germline	clinical testing	Citation Link,
SCV002036450	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001154772

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

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

Benign
(Jul 1, 2024)

germline

clinical testing

Citation Link,

SCV001936704

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Jul 5, 2018)

germline

clinical testing

Citation Link,

SCV002036450

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided

Likely benign

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV001154772.6

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

Description

PKHD1: 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		1	not provided	not provided	not provided

From GeneDx, SCV001936704.1

#	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 Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV002036450.1

#	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

Last Updated: Oct 20, 2024

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