2-86974217-C-T

Variant names:

• chr2-86974217-C-T
• NM_001382344.1:c.1418C>T

Variant summary

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

The NM_001382344.1(RGPD1):​c.1418C>T​(p.Thr473Ile) variant causes a missense change. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 16)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RGPD1 NM_001382344.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 5.36

Genes affected

RGPD1 (HGNC:32414): (RANBP2 like and GRIP domain containing 1) Predicted to contribute to GTPase activator activity. Predicted to be involved in NLS-bearing protein import into nucleus. Predicted to be part of nuclear pore. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RGPD1	NM_001382344.1	c.1418C>T	p.Thr473Ile	missense_variant	Exon 10 of 23	ENST00000641458.2	NP_001369273.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RGPD1	ENST00000641458.2	c.1418C>T	p.Thr473Ile	missense_variant	Exon 10 of 23		NM_001382344.1	ENSP00000492954.1
RGPD1	ENST00000398193.8	c.1418C>T	p.Thr473Ile	missense_variant	Exon 10 of 23	1		ENSP00000381253.3

Frequencies

GnomAD3 genomes Cov.: 16

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1385336 Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0 AN XY: 689850

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 16

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jul 22, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1394C>T (p.T465I) alteration is located in exon 10 (coding exon 10) of the RGPD1 gene. This alteration results from a C to T substitution at nucleotide position 1394, causing the threonine (T) at amino acid position 465 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.51
BayesDel_addAF	Benign	0.0092	T
BayesDel_noAF	Benign	-0.22
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.27	T;.;T;.
Eigen	Uncertain	0.25
Eigen_PC	Benign	0.17
FATHMM_MKL	Uncertain	0.87	D
LIST_S2	Uncertain	0.95	D;D;.;D
M_CAP	Benign	0.052	D
MetaRNN	Uncertain	0.44	T;T;T;T
MetaSVM	Uncertain	0.071	D
MutationAssessor	Uncertain	2.6	M;.;M;.
PrimateAI	Pathogenic	0.84	D
PROVEAN	Uncertain	-3.9	D;D;D;.
REVEL	Uncertain	0.46
Sift	Uncertain	0.0030	D;D;D;.
Sift4G	Pathogenic	0.0010	D;D;D;.
Polyphen		0.98	.;D;.;.
Vest4		0.50
MutPred		0.28		.;Loss of disorder (P = 0.0324);.;Loss of disorder (P = 0.0324);
MVP		0.18
ClinPred		0.95	D
GERP RS		2.3
Varity_R		0.33
gMVP		0.079

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-87201340;