NM_001083116.3(PRF1):c.1265T>C (p.Ile422Thr) AND Familial hemophagocytic lymphohistiocytosis 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 10, 2022
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:: RCV001899635.6

Allele description [Variation Report for NM_001083116.3(PRF1):c.1265T>C (p.Ile422Thr)]

NM_001083116.3(PRF1):c.1265T>C (p.Ile422Thr)

Gene:

PRF1:perforin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q22.1

Genomic location:

Preferred name:

NM_001083116.3(PRF1):c.1265T>C (p.Ile422Thr)

HGVS:

NC_000010.11:g.70598456A>G
NG_009615.1:g.9320T>C
NM_001083116.3:c.1265T>CMANE SELECT
NM_005041.6:c.1265T>C
NP_001076585.1:p.Ile422Thr
NP_005032.2:p.Ile422Thr
LRG_94:g.9320T>C
NC_000010.10:g.72358212A>G

Protein change:

I422T

Links:

dbSNP: rs2132475412

NCBI 1000 Genomes Browser:

rs2132475412

Molecular consequence:

NM_001083116.3:c.1265T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_005041.6:c.1265T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Familial hemophagocytic lymphohistiocytosis 2 (FHL2)
Identifiers:: MONDO: MONDO:0011337; MedGen: C1863727; Orphanet: 540; OMIM: 603553

Recent activity

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VOC family protein [Olsenella uli]
VOC family protein [Olsenella uli]
gi|503017065|ref|WP_013252041.1|

Protein
Mus musculus proline rich 13 (Prr13), transcript variant 1, mRNA
Mus musculus proline rich 13 (Prr13), transcript variant 1, mRNA
gi|283945464|ref|NM_025385.3|

Nucleotide
Homo sapiens small nucleolar RNA, H/ACA box 11B (SNORA11B), small nucleolar RNA
Homo sapiens small nucleolar RNA, H/ACA box 11B (SNORA11B), small nucleolar RNA
gi|156564418|ref|NR_003709.1|

Nucleotide
RecName: Full=Immunoglobulin heavy variable 3-64; Flags: Precursor
RecName: Full=Immunoglobulin heavy variable 3-64; Flags: Precursor
gi|1109545979|sp|A0A075B6Q5.1|HV364 N

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002146145	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 10, 2022)	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

SCV002146145

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 10, 2022)

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, SCV002146145.3

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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. This variant has not been reported in the literature in individuals affected with PRF1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 422 of the PRF1 protein (p.Ile422Thr).

#	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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