chr7-30135226-G-T

Position:

• chr7-30135226-G-T

Variant summary

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

The NM_152793.3(MTURN):​c.90G>T​(p.Arg30Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: MTURN NM_152793.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.23

Genes affected

MTURN (HGNC:25457): (maturin, neural progenitor differentiation regulator homolog) Involved in negative regulation of NF-kappaB transcription factor activity; positive regulation of MAPK cascade; and positive regulation of megakaryocyte differentiation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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/exons	MANE	Protein	UniProt
MTURN	NM_152793.3	c.90G>T	p.Arg30Ser	missense_variant	1/3	ENST00000324453.13	NP_690006.2
MTURN	XM_005249652.4	c.90G>T	p.Arg30Ser	missense_variant	1/4		XP_005249709.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTURN	ENST00000324453.13	c.90G>T	p.Arg30Ser	missense_variant	1/3	1	NM_152793.3	ENSP00000324204	P1
MTURN	ENST00000409688.1	c.90G>T	p.Arg30Ser	missense_variant	1/2	2		ENSP00000386490

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1369874 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 680942

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

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

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 11, 2024

The c.90G>T (p.R30S) alteration is located in exon 1 (coding exon 1) of the MTURN gene. This alteration results from a G to T substitution at nucleotide position 90, causing the arginine (R) at amino acid position 30 to be replaced by a serine (S). 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	1.0
BayesDel_addAF	Pathogenic	0.33	D
BayesDel_noAF	Pathogenic	0.23
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.14	T;.
Eigen	Benign	0.19
Eigen_PC	Benign	0.17
FATHMM_MKL	Uncertain	0.78	D
LIST_S2	Uncertain	0.88	D;D
M_CAP	Pathogenic	0.89	D
MetaRNN	Uncertain	0.53	D;D
MetaSVM	Benign	-0.87	T
MutationAssessor	Benign	0.69	N;N
MutationTaster	Benign	1.0	D;D;D
PROVEAN	Uncertain	-3.7	D;D
REVEL	Uncertain	0.43
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0	D;D
Polyphen		0.94	P;.
Vest4		0.51
MutPred		0.29		Gain of phosphorylation at R30 (P = 0.0731);Gain of phosphorylation at R30 (P = 0.0731);
MVP		0.23
MPC		1.9
ClinPred		0.98	D
GERP RS		3.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.76
gMVP		0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-30174842;