3-52662252-C-G

Variant names:

• chr3-52662252-C-G
• ENST00000707071.1:c.409G>C

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2 PP3_Strong

The NM_001405601.1(PBRM1):​c.409G>C​(p.Ala137Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PBRM1 NM_001405601.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.36

Genes affected

PBRM1 (HGNC:30064): (polybromo 1) This locus encodes a subunit of ATP-dependent chromatin-remodeling complexes. The encoded protein has been identified as in integral component of complexes necessary for ligand-dependent transcriptional activation by nuclear hormone receptors. Mutations at this locus have been associated with primary clear cell renal cell carcinoma. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.941

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PBRM1	NM_001405601.1	c.409G>C	p.Ala137Pro	missense_variant	Exon 5 of 32		NP_001392530.1
PBRM1	NM_001405607.1	c.409G>C	p.Ala137Pro	missense_variant	Exon 5 of 32		NP_001392536.1
PBRM1	NM_001405598.1	c.409G>C	p.Ala137Pro	missense_variant	Exon 5 of 31		NP_001392527.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PBRM1	ENST00000707071.1	c.409G>C	p.Ala137Pro	missense_variant	Exon 5 of 32			ENSP00000516722.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Pathogenic	0.20
CADD	Pathogenic	33
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.45	.;.;T;.;.;.;.;.;.;.;T;T
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.96
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.95	D;D;D;D;D;D;D;D;D;D;D;D
M_CAP	Uncertain	0.10	D
MetaRNN	Pathogenic	0.94	D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.22	D
MutationAssessor	Pathogenic	4.4	H;H;H;H;H;H;H;H;.;.;.;.
PrimateAI	Pathogenic	0.83	D
PROVEAN	Pathogenic	-4.5	D;D;D;D;D;D;D;D;D;D;D;D
REVEL	Pathogenic	0.69
Sift	Pathogenic	0.0	D;D;D;D;D;D;D;D;D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;D;D;D;D;.;.;.;.
Polyphen		1.0	D;D;D;D;D;D;D;D;.;.;.;.
Vest4		0.93
MutPred		0.86		Gain of catalytic residue at A137 (P = 0.0284);Gain of catalytic residue at A137 (P = 0.0284);Gain of catalytic residue at A137 (P = 0.0284);Gain of catalytic residue at A137 (P = 0.0284);Gain of catalytic residue at A137 (P = 0.0284);Gain of catalytic residue at A137 (P = 0.0284);Gain of catalytic residue at A137 (P = 0.0284);Gain of catalytic residue at A137 (P = 0.0284);Gain of catalytic residue at A137 (P = 0.0284);.;Gain of catalytic residue at A137 (P = 0.0284);Gain of catalytic residue at A137 (P = 0.0284);
MVP		0.81
MPC		1.6
ClinPred		1.0	D
GERP RS		5.5
Varity_R		0.98
gMVP		0.94

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-52696268;