NM_031448.6(C19orf12):c.221C>G (p.Pro74Arg) AND Hereditary spastic paraplegia 43

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 2, 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:: RCV002237734.4

Allele description [Variation Report for NM_031448.6(C19orf12):c.221C>G (p.Pro74Arg)]

NM_031448.6(C19orf12):c.221C>G (p.Pro74Arg)

Gene:

C19orf12:chromosome 19 open reading frame 12 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q12

Genomic location:

Preferred name:

NM_031448.6(C19orf12):c.221C>G (p.Pro74Arg)

HGVS:

NC_000019.10:g.29702917G>C
NG_031970.2:g.17873C>G
NM_001031726.4:c.221C>G
NM_001256046.3:c.221C>G
NM_001256047.2:c.221C>G
NM_001282929.1:c.29C>G
NM_001282930.3:c.29C>G
NM_001282931.3:c.29C>G
NM_031448.6:c.221C>GMANE SELECT
NP_001026896.3:p.Pro74Arg
NP_001242975.1:p.Pro74Arg
NP_001242976.1:p.Pro74Arg
NP_001269858.1:p.Pro10Arg
NP_001269859.1:p.Pro10Arg
NP_001269860.1:p.Pro10Arg
NP_113636.2:p.Pro74Arg
NC_000019.9:g.30193824G>C

Protein change:

P10R

Links:

dbSNP: rs747900430

NCBI 1000 Genomes Browser:

rs747900430

Molecular consequence:

NM_001031726.4:c.221C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001256046.3:c.221C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001256047.2:c.221C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001282929.1:c.29C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001282930.3:c.29C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001282931.3:c.29C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_031448.6:c.221C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary spastic paraplegia 43
Synonyms:: Spastic paraplegia 43, autosomal recessive
Identifiers:: MONDO: MONDO:0014024; MedGen: C2680446; Orphanet: 320370; OMIM: 615043

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002510941	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 2, 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

SCV002510941

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 2, 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, SCV002510941.3

#	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. ClinVar contains an entry for this variant (Variation ID: 1682828). This variant has not been reported in the literature in individuals affected with C19orf12-related conditions. This variant is present in population databases (rs747900430, gnomAD 0.02%). This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 85 of the C19orf12 protein (p.Pro85Arg).

#	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: Oct 20, 2024

ClinVar

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