dbSNP rs2074252305: MAP7D3:p.Ile581Phe (chrX-136230394-T-A) – 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_024597.4(MAP7D3):c.1741A>T(p.Ile581Phe) 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: 22)

Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

MAP7D3
NM_024597.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.394

Publications

0 publications found

Variant links:

Genes affected

MAP7D3 (HGNC:25742): (MAP7 domain containing 3) The protein encoded by this gene belongs to the MAP7 (microtubule-associated protein 7) family. Alternatively spliced transcript variants encoding different isoforms have been found. [provided by RefSeq, Mar 2010]

MAP7D3 Gene-Disease associations (from GenCC):

neurodevelopmental disorder
Inheritance: XL Classification: LIMITED Submitted by: Ambry Genetics

MAP7D3 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=0.11102691).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024597.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MAP7D3	NM_024597.4	MANE Select	c.1741A>T	p.Ile581Phe	missense	Exon 10 of 19	NP_078873.2
MAP7D3	NM_001173516.1		c.1687A>T	p.Ile563Phe	missense	Exon 10 of 19	NP_001166987.1	Q8IWC1-4
MAP7D3	NM_001173517.2		c.1636A>T	p.Ile546Phe	missense	Exon 9 of 18	NP_001166988.1	Q8IWC1-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MAP7D3	ENST00000316077.14	TSL:1 MANE Select	c.1741A>T	p.Ile581Phe	missense	Exon 10 of 19	ENSP00000318086.9	Q8IWC1-1
MAP7D3	ENST00000370661.5	TSL:1	c.1636A>T	p.Ile546Phe	missense	Exon 9 of 18	ENSP00000359695.1	Q8IWC1-3
MAP7D3	ENST00000370660.3	TSL:1	c.1618A>T	p.Ile540Phe	missense	Exon 10 of 17	ENSP00000359694.3	A0A0A0MRP0

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1053451

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

327889

African (AFR)

AF:

0.00

AC:

AN:

25443

American (AMR)

AF:

0.00

AC:

AN:

34832

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19070

East Asian (EAS)

AF:

0.00

AC:

AN:

30003

South Asian (SAS)

AF:

0.00

AC:

AN:

52562

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40434

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3996

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

802426

Other (OTH)

AF:

0.00

AC:

AN:

44685

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000151

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

0.24

BayesDel_addAF

Benign

-0.30

BayesDel_noAF

Benign

-0.67

CADD

Benign

(source)

DANN

Benign

0.97

DEOGEN2

Benign

0.027

FATHMM_MKL

Benign

0.077

LIST_S2

Benign

0.72

M_CAP

Benign

0.0030

MetaRNN

Benign

0.11

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.97

PhyloP100

-0.39

PrimateAI

Benign

0.35

PROVEAN

Benign

-2.1

REVEL

Benign

0.073

Sift

Uncertain

0.0010

Sift4G

Benign

0.11

Polyphen

0.93

Vest4

0.19

MutPred

0.33

Loss of MoRF binding (P = 0.1492)

MVP

0.14

MPC

0.19

ClinPred

0.15

GERP RS

-0.81

Varity_R

0.19

gMVP

0.042

Mutation Taster

=98/2

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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