13-113209730-G-T

Variant names:

• chr13-113209730-G-T
• rs1163049031
• NM_001008895.4:c.103G>T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001008895.4(CUL4A):​c.103G>T​(p.Gly35Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000197 in 1,016,484 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.0000020 (0 hom.)
• Consequence: CUL4A NM_001008895.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.77

Genes affected

CUL4A (HGNC:2554): (cullin 4A) CUL4A is the ubiquitin ligase component of a multimeric complex involved in the degradation of DNA damage-response proteins (Liu et al., 2009 [PubMed 19481525]).[supplied by OMIM, Oct 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CUL4A	NM_001008895.4	c.103G>T	p.Gly35Trp	missense_variant	Exon 1 of 20	ENST00000375440.9	NP_001008895.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CUL4A	ENST00000375440.9	c.103G>T	p.Gly35Trp	missense_variant	Exon 1 of 20	1	NM_001008895.4	ENSP00000364589.4

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 0.00000197 AC: 2 AN: 1016484 Hom.: 0 Cov.: 30 AF XY: 0.00000209 AC XY: 1 AN XY: 479360

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000228

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 30

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.40
BayesDel_addAF	Benign	-0.014	T
BayesDel_noAF	Benign	-0.26
CADD	Pathogenic	27
DANN	Uncertain	0.99
DEOGEN2	Benign	0.15	T;.
Eigen	Benign	0.080
Eigen_PC	Benign	-0.055
FATHMM_MKL	Benign	0.75	D
LIST_S2	Benign	0.58	T;T
M_CAP	Pathogenic	0.58	D
MetaRNN	Uncertain	0.54	D;D
MetaSVM	Benign	-0.76	T
MutationAssessor	Uncertain	2.5	M;.
PrimateAI	Pathogenic	0.90	D
PROVEAN	Benign	-1.4	N;.
REVEL	Benign	0.23
Sift	Uncertain	0.0020	D;.
Sift4G	Uncertain	0.0080	D;D
Polyphen		0.99	D;.
Vest4		0.39
MutPred		0.41		Gain of catalytic residue at A37 (P = 0);Gain of catalytic residue at A37 (P = 0);
MVP		0.85
MPC		0.72
ClinPred		0.81	D
GERP RS		3.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Varity_R		0.085
gMVP		0.27

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1163049031; hg19: chr13-113864044;