1-36172503-C-T

Variant summary

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

The NM_001388490.1(MAP7D1):​c.500C>T​(p.Ala167Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000138 in 1,448,504 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

MAP7D1
NM_001388490.1 missense

Scores

4
12
3

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.03
Variant links:
Genes affected
MAP7D1 (HGNC:25514): (MAP7 domain containing 1) Predicted to be involved in microtubule cytoskeleton organization. Located in cytosol and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAP7D1NM_001388490.1 linkc.500C>T p.Ala167Val missense_variant Exon 4 of 17 ENST00000474796.2 NP_001375419.1
MAP7D1NM_018067.5 linkc.500C>T p.Ala167Val missense_variant Exon 4 of 17 NP_060537.3 Q3KQU3-1
MAP7D1NM_001286366.2 linkc.500C>T p.Ala167Val missense_variant Exon 4 of 18 NP_001273295.1 Q3KQU3-4B3KU03
MAP7D1NM_001286365.2 linkc.500C>T p.Ala167Val missense_variant Exon 4 of 16 NP_001273294.1 Q3KQU3-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAP7D1ENST00000474796.2 linkc.500C>T p.Ala167Val missense_variant Exon 4 of 17 2 NM_001388490.1 ENSP00000507044.1 D3DPS3

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000819
AC:
2
AN:
244254
Hom.:
0
AF XY:
0.0000150
AC XY:
2
AN XY:
132932
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000110
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000138
AC:
2
AN:
1448504
Hom.:
0
Cov.:
30
AF XY:
0.00000278
AC XY:
2
AN XY:
718728
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000508
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.:
33
Bravo
AF:
0.00000756
ExAC
AF:
0.00000824
AC:
1

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Oct 25, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.500C>T (p.A167V) alteration is located in exon 4 (coding exon 4) of the MAP7D1 gene. This alteration results from a C to T substitution at nucleotide position 500, causing the alanine (A) at amino acid position 167 to be replaced by a valine (V). 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
Pathogenic
0.90
BayesDel_addAF
Uncertain
0.056
T
BayesDel_noAF
Uncertain
0.070
CADD
Pathogenic
28
DANN
Pathogenic
1.0
DEOGEN2
Uncertain
0.45
.;.;.;T;.
Eigen
Pathogenic
0.82
Eigen_PC
Pathogenic
0.80
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Uncertain
0.96
D;D;D;D;D
M_CAP
Benign
0.021
T
MetaRNN
Uncertain
0.50
T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.8
.;M;M;M;.
PrimateAI
Uncertain
0.67
T
PROVEAN
Uncertain
-3.9
D;D;D;D;D
REVEL
Uncertain
0.40
Sift
Uncertain
0.0010
D;D;D;D;D
Sift4G
Uncertain
0.021
D;D;D;D;D
Polyphen
1.0, 1.0
.;D;D;D;.
Vest4
0.78, 0.77, 0.80
MutPred
0.35
.;Gain of methylation at K166 (P = 0.0392);Gain of methylation at K166 (P = 0.0392);Gain of methylation at K166 (P = 0.0392);.;
MVP
0.19
MPC
0.57
ClinPred
0.95
D
GERP RS
5.4
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.55
gMVP
0.34

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs142245111; hg19: chr1-36638104; API