22-42808886-T-A

Position:

• chr22-42808886-T-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000263245.10(ARFGAP3):​c.1201A>T​(p.Thr401Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: ARFGAP3 ENST00000263245.10 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.409

Genes affected

ARFGAP3 (HGNC:661): (ADP ribosylation factor GTPase activating protein 3) The protein encoded by this gene is a GTPase-activating protein (GAP) that associates with the Golgi apparatus and regulates the early secretory pathway of proteins. The encoded protein promotes hydrolysis of ADP-ribosylation factor 1 (ARF1)-bound GTP, which is required for the dissociation of coat proteins from Golgi-derived membranes and vesicles. Dissociation of the coat proteins is a prerequisite for the fusion of these vesicles with target compartments. The activity of this protein is sensitive to phospholipids. Multiple transcript variants encoding different isoforms have been found for this gene. This gene was originally known as ARFGAP1, but that is now the name of a related but different gene. [provided by RefSeq, Nov 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.06917292).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARFGAP3	NM_014570.5	c.1201A>T	p.Thr401Ser	missense_variant	13/16	ENST00000263245.10	NP_055385.3
ARFGAP3	NM_001142293.2	c.1069A>T	p.Thr357Ser	missense_variant	12/15		NP_001135765.1
ARFGAP3	XM_005261525.5	c.1069A>T	p.Thr357Ser	missense_variant	12/15		XP_005261582.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARFGAP3	ENST00000263245.10	c.1201A>T	p.Thr401Ser	missense_variant	13/16	1	NM_014570.5	ENSP00000263245.5
ARFGAP3	ENST00000437119.6	c.1069A>T	p.Thr357Ser	missense_variant	12/15	1		ENSP00000388791.2
ARFGAP3	ENST00000453516.5	c.607A>T	p.Thr203Ser	missense_variant	7/8	3		ENSP00000403995.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 02, 2023

The c.1201A>T (p.T401S) alteration is located in exon 13 (coding exon 13) of the ARFGAP3 gene. This alteration results from a A to T substitution at nucleotide position 1201, causing the threonine (T) at amino acid position 401 to be replaced by a serine (S). 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	Benign	0.075
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.9
DANN	Benign	0.84
DEOGEN2	Benign	0.0066	T;.
Eigen	Benign	-0.66
Eigen_PC	Benign	-0.77
FATHMM_MKL	Benign	0.21	N
LIST_S2	Benign	0.70	T;T
M_CAP	Benign	0.0049	T
MetaRNN	Benign	0.069	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.53	N;.
MutationTaster	Benign	1.0	N;N;N
PrimateAI	Benign	0.22	T
PROVEAN	Benign	-0.66	N;N
REVEL	Benign	0.013
Sift	Benign	0.53	T;T
Sift4G	Benign	0.35	T;T
Polyphen		0.0030	B;.
Vest4		0.20
MutPred		0.13		Loss of glycosylation at T401 (P = 0.0556);.;
MVP		0.29
MPC		0.080
ClinPred		0.016	T
GERP RS		0.75
Varity_R		0.059
gMVP		0.18

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: chr22-43204892;