NM_001388490.1:c.106C>G

Variant names:

• chr1-36171030-C-G
• rs779828198
• NM_001388490.1:c.106C>G

Variant summary

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

The NM_001388490.1(MAP7D1):​c.106C>G​(p.Pro36Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000563 in 1,421,694 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P36S) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 29)
  • Exomes 𝑓: 0.0000056 (0 hom.)
• Consequence: MAP7D1 NM_001388490.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.32
• Publications: 2 publications found

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]

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=0.07782915).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP7D1	NM_001388490.1	c.106C>G	p.Pro36Ala	missense_variant	Exon 2 of 17	ENST00000474796.2	NP_001375419.1
MAP7D1	NM_018067.5	c.106C>G	p.Pro36Ala	missense_variant	Exon 2 of 17		NP_060537.3
MAP7D1	NM_001286366.2	c.106C>G	p.Pro36Ala	missense_variant	Exon 2 of 18		NP_001273295.1
MAP7D1	NM_001286365.2	c.106C>G	p.Pro36Ala	missense_variant	Exon 2 of 16		NP_001273294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP7D1	ENST00000474796.2	c.106C>G	p.Pro36Ala	missense_variant	Exon 2 of 17	2	NM_001388490.1	ENSP00000507044.1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome AF: 0.00000563 AC: 8 AN: 1421694 Hom.: 0 Cov.: 29 AF XY: 0.00000848 AC XY: 6 AN XY: 707866

African (AFR) AF: 0.00 AC: 0 AN: 32644

American (AMR) AF: 0.00 AC: 0 AN: 43460

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25104

East Asian (EAS) AF: 0.00 AC: 0 AN: 38340

South Asian (SAS) AF: 0.00 AC: 0 AN: 84852

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52338

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5608

European-Non Finnish (NFE) AF: 0.00000740 AC: 8 AN: 1080822

Other (OTH) AF: 0.00 AC: 0 AN: 58526

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.077
BayesDel_addAF	Benign	-0.15	T
BayesDel_noAF	Benign	-0.46
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.011	.;.;T
Eigen	Benign	-0.043
Eigen_PC	Benign	0.10
FATHMM_MKL	Uncertain	0.82	D
LIST_S2	Benign	0.83	T;D;D
M_CAP	Benign	0.0032	T
MetaRNN	Benign	0.078	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.6	L;L;L
PhyloP100		4.3
PrimateAI	Uncertain	0.61	T
PROVEAN	Benign	-1.3	N;N;N
REVEL	Benign	0.039
Sift	Uncertain	0.024	D;D;D
Sift4G	Benign	0.75	T;T;T
Polyphen		0.093	B;B;B
Vest4		0.36
MutPred		0.27		Loss of glycosylation at P36 (P = 0.0013);Loss of glycosylation at P36 (P = 0.0013);Loss of glycosylation at P36 (P = 0.0013);
MVP		0.10
MPC		0.55
ClinPred		0.79	D
GERP RS		4.9
Varity_R		0.056
gMVP		0.20
Mutation Taster		=96/4	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

Other links and lift over

dbSNP: rs779828198; hg19: chr1-36636631;