chr2-235494840-G-T

Position:

• chr2-235494840-G-T

Variant summary

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

The NM_001037131.3(AGAP1):​c.154G>T​(p.Ala52Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000705 in 1,418,086 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 29)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: AGAP1 NM_001037131.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.86

Genes affected

AGAP1 (HGNC:16922): (ArfGAP with GTPase domain, ankyrin repeat and PH domain 1) This gene encodes a member of an ADP-ribosylation factor GTPase-activating protein family involved in membrane trafficking and cytoskeleton dynamics. This gene functions as a direct regulator of the adaptor-related protein complex 3 on endosomes. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

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=0.11369529).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGAP1	NM_001037131.3	c.154G>T	p.Ala52Ser	missense_variant	1/18	ENST00000304032.13	NP_001032208.1
AGAP1	NM_014914.5	c.154G>T	p.Ala52Ser	missense_variant	1/17		NP_055729.2
AGAP1	NM_001244888.2	c.154G>T	p.Ala52Ser	missense_variant	1/10		NP_001231817.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AGAP1	ENST00000304032.13	c.154G>T	p.Ala52Ser	missense_variant	1/18	5	NM_001037131.3	ENSP00000307634

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome AF: 7.05e-7 AC: 1 AN: 1418086 Hom.: 0 Cov.: 32 AF XY: 0.00000142 AC XY: 1 AN XY: 705456

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: 9.17e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 29

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Mar 12, 2023

This sequence change replaces alanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 52 of the AGAP1 protein (p.Ala52Ser). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant  is likely to be tolerated. This variant has not been reported in the literature in individuals affected with AGAP1-related conditions. This variant is not present in population databases (gnomAD no frequency). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.089
BayesDel_addAF	Benign	-0.084	T
BayesDel_noAF	Benign	-0.36
CADD	Uncertain	24
DANN	Benign	0.95
DEOGEN2	Benign	0.026	.;.;T
Eigen	Benign	-0.50
Eigen_PC	Benign	-0.26
FATHMM_MKL	Benign	0.75	D
LIST_S2	Benign	0.70	T;T;T
M_CAP	Pathogenic	0.75	D
MetaRNN	Benign	0.11	T;T;T
MetaSVM	Benign	-0.75	T
MutationAssessor	Benign	-0.20	N;N;N
MutationTaster	Benign	0.88	D;D;D
PrimateAI	Uncertain	0.79	T
PROVEAN	Benign	-0.16	N;N;N
REVEL	Benign	0.15
Sift	Benign	0.57	T;T;T
Sift4G	Benign	0.89	T;T;T
Polyphen		0.0010, 0.0	.;B;B
Vest4		0.055
MutPred		0.23		Gain of phosphorylation at A52 (P = 0.1617);Gain of phosphorylation at A52 (P = 0.1617);Gain of phosphorylation at A52 (P = 0.1617);
MVP		0.48
MPC		0.38
ClinPred		0.40	T
GERP RS		4.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.081
gMVP		0.28

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: rs1255540343; hg19: chr2-236403484;