MAP6D1 p.Gly90Arg

Variant names:

• chr3-183825280-C-G
• rs972388049
• NM_024871.4:c.268G>C
• MAP6D1 p.Gly90Arg

Your query was ambiguous. Multiple possible variants found:

• chr3-183825280-C-G
• chr3-183825280-C-T
• chr3-183825278-TCC-ACG
• chr3-183825278-TCC-GCG
• chr3-183825278-TCC-CCG
• chr3-183825278-TCC-CCT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_024871.4(MAP6D1):​c.268G>C​(p.Gly90Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000843 in 1,185,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 8.4e-7 (0 hom.)
• Consequence: MAP6D1 NM_024871.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 0 publications found

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]

ENSG00000283765 (HGNC:):

ACMG classification

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=0.097447634).

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>C	p.Gly90Arg	missense	Exon 1 of 3	NP_079147.1	Q9H9H5

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 8.43e-7 AC: 1 AN: 1185888 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 573636

African (AFR) AF: 0.00 AC: 0 AN: 23404

American (AMR) AF: 0.00 AC: 0 AN: 8842

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15826

East Asian (EAS) AF: 0.00 AC: 0 AN: 26922

South Asian (SAS) AF: 0.00 AC: 0 AN: 42268

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38130

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4098

European-Non Finnish (NFE) AF: 0.00000102 AC: 1 AN: 978298

Other (OTH) AF: 0.00 AC: 0 AN: 48100

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	9.7
DANN	Benign	0.97
DEOGEN2	Benign	0.025	T
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.038	N
LIST_S2	Benign	0.40	T
M_CAP	Benign	0.067	D
MetaRNN	Benign	0.097	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.4	M
PhyloP100		-0.31
PrimateAI	Uncertain	0.78	T
PROVEAN	Benign	-1.2	N
REVEL	Benign	0.058
Sift	Benign	0.091	T
Sift4G	Uncertain	0.023	D
PromoterAI		0.087	Neutral
Varity_R		0.053
gMVP		0.13
Mutation Taster		=98/2	polymorphism

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs972388049; hg19: chr3-183543068;