Genetic Variant SLC33A2:p.Arg199Cys (chr8-144509928-CGT-TGC) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is The variant received 2 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_Moderate

The NM_138431.3(SLC33A2):c.595_597delCGTinsTGC (p.Arg199Cys) variant causes a missense change. Note: allele frequency estimates from gnomAD may be inaccurate for this variant type (MNP or indel longer than 3 bp) due to technology limitations. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Other variants at the same amino acid position have been reported in ClinVar (not pathogenic): p.R199C: Uncertain_significance (ClinVar VariationId 2392771, 1 star)

Frequency

Genomes: not found (cov: 34)

Consequence

SLC33A2
NM_138431.3 missense

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.322

Publications

0 publications found

Variant links:

Genes affected

SLC33A2 (HGNC:25157): (solute carrier family 33 member 2) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jun 2026]

SLC33A2 links:

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new If you want to explore the variant's impact on the transcript NM_138431.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 2 points.

Show applied only (1)

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	O3Absent or very rare in population		Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = absent, AC = 0 — absent/extremely rare (O3 moderate [+2])

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_138431.3. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	SLC33A2 NM_138431.3	MANE Select	c.595_597delCGTinsTGC p.Arg199Cys	missense	N/A	Prot: NP_612440.1 UniProt: Q96ES6
	SLC33A2 NR_130120.2		n.859_861delCGTinsTGC	non_coding_transcript_exon	Exon 1 of 4	Prot:

SLC33A2 NM_138431.3

MANE Select

HGVSc / HGVSpc.595_597delCGTinsTGCp.Arg199Cys

Exon rankN/A

missense

Prot: NP_612440.1UniProt: Q96ES6

SLC33A2 NR_130120.2

HGVSc / HGVSpn.859_861delCGTinsTGC

Exon rankExon 1 of 4

non_coding_transcript_exon

Prot:

Ensembl Transcripts

Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
MFSD3 ENST00000301327.5	TSL:1MANE Select	c.595_597delCGTinsTGC p.Arg199Cys	missense	N/A	Prot: ENSP00000301327.3 UniProt: Q96ES6
MFSD3 ENST00000883534.1		c.595_597delCGTinsTGC p.Arg199Cys	missense	N/A	Prot: ENSP00000553593.1 UniProt: A0ACI8RL54
MFSD3 ENST00000526749.1	TSL:2	n.310_312delCGTinsTGC	non_coding_transcript_exon	Exon 1 of 2	Prot:

MFSD3 ENST00000301327.5

TSL:1MANE Select

HGVSc / HGVSpc.595_597delCGTinsTGCp.Arg199Cys

Exon rankN/A

missense

Prot: ENSP00000301327.3UniProt: Q96ES6

MFSD3 ENST00000883534.1

HGVSc / HGVSpc.595_597delCGTinsTGCp.Arg199Cys

Exon rankN/A

missense

Prot: ENSP00000553593.1UniProt: A0ACI8RL54

MFSD3 ENST00000526749.1

TSL:2

HGVSc / HGVSpn.310_312delCGTinsTGC

Exon rankExon 1 of 2

non_coding_transcript_exon

Prot:

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 2 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:34
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:34

Showing 2 sources

Tested, but no data found:GnomAD4 exomeIf GnomAD4 is missing, the position is probably not covered by the project.

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
PhyloP100	Benign	-0.32

Showing 1 of 1 scores

Splicing Scores

No splicing scores have been computed for this variant.

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACGS-UK Somatic Oncogenicity v2025

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

MaveDB functional evidence ?

Publications

Other links and lift over

MaveDB functional evidence