NM_001128205.2(SULF1):c.2012A>C (p.Lys671Thr) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 9, 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:: RCV003552241.2

Allele description [Variation Report for NM_001128205.2(SULF1):c.2012A>C (p.Lys671Thr)]

NM_001128205.2(SULF1):c.2012A>C (p.Lys671Thr)

Gene:

SULF1:sulfatase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q13.3

Genomic location:

Preferred name:

NM_001128205.2(SULF1):c.2012A>C (p.Lys671Thr)

HGVS:

NC_000008.11:g.69627836A>C
NG_042849.1:g.166213A>C
NM_001128204.2:c.2012A>C
NM_001128205.2:c.2012A>CMANE SELECT
NM_001128206.2:c.2012A>C
NM_001412828.1:c.2012A>C
NM_001412829.1:c.2012A>C
NM_001412830.1:c.2012A>C
NM_001412831.1:c.2012A>C
NM_001412832.1:c.1883A>C
NM_001412833.1:c.2012A>C
NM_001412834.1:c.2012A>C
NM_001412835.1:c.2012A>C
NM_001412836.1:c.1955A>C
NM_001412837.1:c.1955A>C
NM_001412838.1:c.1883A>C
NM_001412839.1:c.1883A>C
NM_001412840.1:c.1883A>C
NM_001412841.1:c.1826A>C
NM_001412842.1:c.1826A>C
NM_001412843.1:c.2012A>C
NM_001412844.1:c.1412A>C
NM_001412845.1:c.1412A>C
NM_001412846.1:c.221A>C
NM_001412850.1:c.2012A>C
NM_001412851.1:c.2012A>C
NM_015170.3:c.2012A>C
NP_001121676.1:p.Lys671Thr
NP_001121677.1:p.Lys671Thr
NP_001121678.1:p.Lys671Thr
NP_001399757.1:p.Lys671Thr
NP_001399758.1:p.Lys671Thr
NP_001399759.1:p.Lys671Thr
NP_001399760.1:p.Lys671Thr
NP_001399761.1:p.Lys628Thr
NP_001399762.1:p.Lys671Thr
NP_001399763.1:p.Lys671Thr
NP_001399764.1:p.Lys671Thr
NP_001399765.1:p.Lys652Thr
NP_001399766.1:p.Lys652Thr
NP_001399767.1:p.Lys628Thr
NP_001399768.1:p.Lys628Thr
NP_001399769.1:p.Lys628Thr
NP_001399770.1:p.Lys609Thr
NP_001399771.1:p.Lys609Thr
NP_001399772.1:p.Lys671Thr
NP_001399773.1:p.Lys471Thr
NP_001399774.1:p.Lys471Thr
NP_001399775.1:p.Lys74Thr
NP_001399779.1:p.Lys671Thr
NP_001399780.1:p.Lys671Thr
NP_055985.2:p.Lys671Thr
NC_000008.10:g.70540071A>C
NR_132437.1:n.1362A>C
NR_156414.2:n.2519A>C
NR_156415.2:n.2681A>C
NR_182050.1:n.2410A>C
NR_182051.1:n.2572A>C
NR_182053.1:n.2565A>C
NR_182055.1:n.2150A>C

Protein change:

K471T

Molecular consequence:

NM_001128204.2:c.2012A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001128205.2:c.2012A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001128206.2:c.2012A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412828.1:c.2012A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412829.1:c.2012A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412830.1:c.2012A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412831.1:c.2012A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412832.1:c.1883A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412833.1:c.2012A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412834.1:c.2012A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412835.1:c.2012A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412836.1:c.1955A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412837.1:c.1955A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412838.1:c.1883A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412839.1:c.1883A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412840.1:c.1883A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412841.1:c.1826A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412842.1:c.1826A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412843.1:c.2012A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412844.1:c.1412A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412845.1:c.1412A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412846.1:c.221A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412850.1:c.2012A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001412851.1:c.2012A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_015170.3:c.2012A>C - missense variant - [Sequence Ontology: SO:0001583]
NR_132437.1:n.1362A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_156414.2:n.2519A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_156415.2:n.2681A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_182050.1:n.2410A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_182051.1:n.2572A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_182053.1:n.2565A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_182055.1:n.2150A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Model organism or animal sample from Coturnix japonica
Model organism or animal sample from Coturnix japonica

biosample
VWA domain-containing protein [Haloplanus salinus]
VWA domain-containing protein [Haloplanus salinus]
gi|1434754263|ref|WP_114450790.1|

Protein
Sporidesmiella hyalosperma voucher MFLU:18-2330 translation elongation factor 1-...
Sporidesmiella hyalosperma voucher MFLU:18-2330 translation elongation factor 1-alpha (tef1) gene, partial cds
gi|1775197989|gb|MN194033.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004263067	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 9, 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

SCV004263067

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 9, 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, SCV004263067.1

#	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 available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. This variant has not been reported in the literature in individuals affected with SULF1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces lysine, which is basic and polar, with threonine, which is neutral and polar, at codon 671 of the SULF1 protein (p.Lys671Thr).

#	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

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