NM_016180.5(SLC45A2):c.656TCT[2] (p.Phe221del) AND not provided

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Aug 24, 2023
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:: RCV002512770.4

Allele description [Variation Report for NM_016180.5(SLC45A2):c.656TCT[2] (p.Phe221del)]

NM_016180.5(SLC45A2):c.656TCT[2] (p.Phe221del)

Gene:

SLC45A2:solute carrier family 45 member 2 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

5p13.2

Genomic location:

Preferred name:

NM_016180.5(SLC45A2):c.656TCT[2] (p.Phe221del)

HGVS:

NC_000005.10:g.33963916GAA[2]
NG_011691.2:g.25753TCT[2]
NM_001012509.4:c.656TCT[2]
NM_001297417.4:c.563-9419TCT[2]
NM_016180.3:c.662_664del
NM_016180.5:c.656TCT[2]MANE SELECT
NP_001012527.2:p.Phe221del
NP_057264.4:p.Phe221del
NC_000005.9:g.33964020_33964022del
NC_000005.9:g.33964021GAA[2]
NG_011691.1:g.25758_25760del
NM_016180.3:c.661_663del

Protein change:

F221del

Links:

OMIM: 606202.0004; dbSNP: rs387906318

NCBI 1000 Genomes Browser:

rs387906318

Molecular consequence:

NM_001012509.4:c.656TCT[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_016180.5:c.656TCT[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001297417.4:c.563-9419TCT[2] - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase [Methanimicrococcus...
tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase [Methanimicrococcus stummii]
gi|2591780233|gnl|goettingen|MmiEs2 0|gb|WNY28366.1|

Protein
Ophidion asiro isolate ASIZP_0910637 rhodopsin (RH) gene, partial cds
Ophidion asiro isolate ASIZP_0910637 rhodopsin (RH) gene, partial cds
gi|2789067012|gb|OR818849.1|

Nucleotide
RecName: Full=tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase
RecName: Full=tRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase
gi|12230744|sp|O67010.1|TRM1_AQUAE

Protein
db38g07.x1 Blackshear/Soares normalized Xenopus egg library Xenopus laevis cDNA ...
db38g07.x1 Blackshear/Soares normalized Xenopus egg library Xenopus laevis cDNA clone IMAGE:3300828 3', mRNA sequence
gi|9610455|gnl|dbEST|5614700|gb|BE4 .1|

Nucleotide
BX712161 XGC-tadpole Xenopus tropicalis cDNA clone TTpA020p05 5', mRNA sequence
BX712161 XGC-tadpole Xenopus tropicalis cDNA clone TTpA020p05 5', mRNA sequence
gi|38387684|gnl|dbEST|20432295|emb| 161.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003525811	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Aug 24, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 14722913, 29345414, 28492532
SCV003933662	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Apr 25, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003525811

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Aug 24, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV003933662

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Apr 25, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Mutations in the MATP gene in five German patients affected by oculocutaneous albinism type 4.

Rundshagen U, Zühlke C, Opitz S, Schwinger E, Käsmann-Kellner B.

Hum Mutat. 2004 Feb;23(2):106-110. doi: 10.1002/humu.10311.

PubMed [citation]

PMID:: 14722913

Molecular characterization of a series of 990 index patients with albinism.

Lasseaux E, Plaisant C, Michaud V, Pennamen P, Trimouille A, Gaston L, Monfermé S, Lacombe D, Rooryck C, Morice-Picard F, Arveiler B.

Pigment Cell Melanoma Res. 2018 Jul;31(4):466-474. doi: 10.1111/pcmr.12688. Epub 2018 Feb 14.

PubMed [citation]

PMID:: 29345414

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003525811.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant, c.662_664del, results in the deletion of 1 amino acid(s) of the SLC45A2 protein (p.Phe221del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). 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. This variant has been observed in individual(s) with clinical features of oculocutaneous albisnism (PMID: 14722913, 29345414; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant.

#	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

From GeneDx, SCV003933662.1

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

Description

Observed with a second SLC45A2 variant in patients with oculocutaneous albinism in published literature, although additional clinical information and segregation data were not provided (Rundshagen et al., 2004; Lasseaux et al., 2018); In-frame deletion of 1 amino acid in a non-repeat region; Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31589614, 30398625, 14722913, 29345414, 34838614)

#	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: Sep 29, 2024

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