NM_001171.6(ABCC6):c.3349T>C (p.Ser1117Pro) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 19, 2023
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:: RCV003704965.2

Allele description [Variation Report for NM_001171.6(ABCC6):c.3349T>C (p.Ser1117Pro)]

NM_001171.6(ABCC6):c.3349T>C (p.Ser1117Pro)

Gene:

ABCC6:ATP binding cassette subfamily C member 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.11

Genomic location:

Preferred name:

NM_001171.6(ABCC6):c.3349T>C (p.Ser1117Pro)

HGVS:

NC_000016.10:g.16163150A>G
NG_007558.3:g.65468T>C
NM_001171.6:c.3349T>CMANE SELECT
NM_001351800.1:c.3007T>C
NP_001162.5:p.Ser1117Pro
NP_001338729.1:p.Ser1003Pro
LRG_1115t1:c.3349T>C
LRG_1115:g.65468T>C
LRG_1115p1:p.Ser1117Pro
NC_000016.9:g.16257007A>G

Protein change:

S1003P

Molecular consequence:

NM_001171.6:c.3349T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001351800.1:c.3007T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

AFV31615 (0)
Biocollections
Homo sapiens discs large MAGUK scaffold protein 2 (DLG2), transcript variant 8, ...
Homo sapiens discs large MAGUK scaffold protein 2 (DLG2), transcript variant 8, mRNA
gi|1800081822|ref|NM_001351275.2|

Nucleotide
YP_001098112 (0)
OMIM
PREDICTED: Mus musculus collagen, type XIII, alpha 1 (Col13a1), transcript varia...
PREDICTED: Mus musculus collagen, type XIII, alpha 1 (Col13a1), transcript variant X10, mRNA
gi|1907073232|ref|XM_011243331.3|

Nucleotide
Arabidopsis thaliana Mannose-binding lectin superfamily protein (RTM1), mRNA
Arabidopsis thaliana Mannose-binding lectin superfamily protein (RTM1), mRNA
gi|1063680640|ref|NM_100456.3|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004467290	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (May 19, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004467290

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(May 19, 2023)

germline

clinical testing

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004467290.1

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

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt ABCC6 protein function. This missense change has been observed in individual(s) with pseudoxanthoma elasticum (Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 1117 of the ABCC6 protein (p.Ser1117Pro).

#	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: Sep 29, 2024

ClinVar

Relating variation to medicine