Genetic Variant RNF20:p.Thr236Pro (chr9-101544844-ACA-CCT) – 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_019592.7(RNF20):c.706_708delACAinsCCT (p.Thr236Pro) variant causes a missense change. The gene RNF20 is a tumor suppressor gene (CancerMine: 3 TSG citations). 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.T236P: Uncertain_significance (ClinVar VariationId 2408106, 1 star)

Frequency

Genomes: not found (cov: 32)

Consequence

RNF20
NM_019592.7 missense

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.28

Publications

0 publications found

Variant links:

Genes affected

RNF20 (HGNC:10062): (ring finger protein 20) The protein encoded by this gene shares similarity with BRE1 of S. cerevisiae. The protein encoded by this human gene is an E3 ubiquitin ligase that regulates chromosome structure by monoubiquitinating histone H2B. This protein acts as a putative tumor suppressor and positively regulates the p53 tumor suppressor as well as numerous histone H2A and H2B genes. In contrast, this protein also suppresses the expression of several protooncogenes and growth-related genes, including many genes that are induced by epidermal growth factor. This gene selectively suppresses the expression of some genes by interfering with chromatin recruitment of transcription elongation factor SII (TFIIS). [provided by RefSeq, Feb 2012]

RNF20 links:

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new If you want to explore the variant's impact on the transcript NM_019592.7, 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_019592.7. 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
	RNF20 NM_019592.7	MANE Select	c.706_708delACAinsCCT p.Thr236Pro	missense	N/A	Prot: NP_062538.5

RNF20 NM_019592.7

MANE Select

HGVSc / HGVSpc.706_708delACAinsCCTp.Thr236Pro

Exon rankN/A

missense

Prot: NP_062538.5

Ensembl Transcripts

Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
RNF20 ENST00000389120.8	TSL:1MANE Select	c.706_708delACAinsCCT p.Thr236Pro	missense	N/A	Prot: ENSP00000373772.3 UniProt: Q5VTR2
RNF20 ENST00000888393.1		c.706_708delACAinsCCT p.Thr236Pro	missense	N/A	Prot: ENSP00000558452.1 UniProt: Q5VTR2
RNF20 ENST00000888394.1		c.706_708delACAinsCCT p.Thr236Pro	missense	N/A	Prot: ENSP00000558453.1 UniProt: Q5VTR2

RNF20 ENST00000389120.8

TSL:1MANE Select

HGVSc / HGVSpc.706_708delACAinsCCTp.Thr236Pro

Exon rankN/A

missense

Prot: ENSP00000373772.3UniProt: Q5VTR2

RNF20 ENST00000888393.1

HGVSc / HGVSpc.706_708delACAinsCCTp.Thr236Pro

Exon rankN/A

missense

Prot: ENSP00000558452.1UniProt: Q5VTR2

RNF20 ENST00000888394.1

HGVSc / HGVSpc.706_708delACAinsCCTp.Thr236Pro

Exon rankN/A

missense

Prot: ENSP00000558453.1UniProt: Q5VTR2

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:32
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 2 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
PhyloP100	Uncertain	4.3

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