Genetic Variant MAP6D1:p.Gly90Arg (chr3-183825280-C-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_024871.4(MAP6D1):c.268G>A(p.Gly90Arg) 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. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MAP6D1
NM_024871.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.314

Publications

0 publications found

Variant links:

Genes affected

MAP6D1 (HGNC:25753): (MAP6 domain containing 1) This gene encodes a protein highly similar to the mouse MAP6 domain containing 1 protein, which is related to the STOP proteins. Based on the study of the mouse protein, the encoded protein may function as a calmodulin-regulated neuronal protein that binds and stabilizes microtubules but also associates with the Golgi membranes through N-terminal palmitoylation. [provided by RefSeq, Oct 2008]

MAP6D1 links:

ENSG00000283765 (HGNC:):

ENSG00000283765 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.09773147).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024871.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP6D1	NM_024871.4	MANE Select	c.268G>A	p.Gly90Arg	missense	Exon 1 of 3	NP_079147.1	Q9H9H5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MAP6D1	ENST00000318631.8	TSL:1 MANE Select	c.268G>A	p.Gly90Arg	missense	Exon 1 of 3	ENSP00000314560.4	Q9H9H5
ENSG00000283765	ENST00000639401.1	TSL:5	c.1029-7169G>A		intron	N/A	ENSP00000491227.1	A0A1W2PP11
MAP6D1	ENST00000933005.1		c.268G>A	p.Gly90Arg	missense	Exon 1 of 4	ENSP00000603064.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1185888

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

573636

African (AFR)

AF:

0.00

AC:

AN:

23404

American (AMR)

AF:

0.00

AC:

AN:

8842

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15826

East Asian (EAS)

AF:

0.00

AC:

AN:

26922

South Asian (SAS)

AF:

0.00

AC:

AN:

42268

European-Finnish (FIN)

AF:

0.00

AC:

AN:

38130

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4098

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

978298

Other (OTH)

AF:

0.00

AC:

AN:

48100

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Benign

-0.58

CADD

Benign

(source)

DANN

Uncertain

0.97

DEOGEN2

Benign

0.025

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.038

LIST_S2

Benign

0.40

M_CAP

Benign

0.067

MetaRNN

Benign

0.098

MetaSVM

Benign

-1.0

MutationAssessor

Uncertain

2.4

PhyloP100

-0.31

PrimateAI

Uncertain

0.78

PROVEAN

Benign

-1.2

REVEL

Benign

0.058

Sift

Benign

0.091

Sift4G

Uncertain

0.023

Polyphen

0.0030

Vest4

0.049

MutPred

0.23

Gain of methylation at G90 (P = 0.0148)

MVP

0.27

MPC

0.0083

ClinPred

0.26

GERP RS

-5.1

PromoterAI

-0.023

Neutral

(source)

Varity_R

0.053

gMVP

0.13

Mutation Taster

=98/2

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over