NM_019556.3:c.395G>T

Variant names:

• chrX-134896870-C-A
• NM_019556.3:c.395G>T

Variant summary

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

The NM_019556.3(MOSPD1):​c.395G>T​(p.Arg132Ile) variant causes a missense change involving the alteration of a 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: 23)
• Consequence: MOSPD1 NM_019556.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.46
• Publications: 0 publications found

Genes affected

MOSPD1 (HGNC:25235): (motile sperm domain containing 1) Predicted to be involved in negative regulation of transcription by RNA polymerase II and positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleus and perinuclear region of cytoplasm. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019556.3. 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
	MOSPD1	NM_019556.3	MANE Select	c.395G>T	p.Arg132Ile	missense	Exon 4 of 6	NP_062456.1	Q9UJG1-1
	MOSPD1	NM_001306188.2		c.395G>T	p.Arg132Ile	missense	Exon 4 of 5	NP_001293117.1	Q9UJG1-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOSPD1	ENST00000370783.8	TSL:1 MANE Select	c.395G>T	p.Arg132Ile	missense	Exon 4 of 6	ENSP00000359819.3	Q9UJG1-1
	MOSPD1	ENST00000491609.5	TSL:1	n.470G>T		non_coding_transcript_exon	Exon 3 of 5
	MOSPD1	ENST00000370777.1	TSL:5	c.395G>T	p.Arg132Ile	missense	Exon 3 of 5	ENSP00000359813.1	Q9UJG1-3

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 23

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Pathogenic	0.25	D
BayesDel_noAF	Uncertain	0.12
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.024	T
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Uncertain	0.95	D
M_CAP	Pathogenic	0.84	D
MetaRNN	Uncertain	0.74	D
MetaSVM	Benign	-0.46	T
MutationAssessor	Benign	1.4	L
PhyloP100		7.5
PrimateAI	Uncertain	0.63	T
PROVEAN	Benign	-1.1	N
REVEL	Benign	0.28
Sift	Benign	0.11	T
Sift4G	Benign	0.18	T
Polyphen		0.34	B
Vest4		0.62
MutPred		0.33		Loss of solvent accessibility (P = 0.01)
MVP		0.77
MPC		2.1
ClinPred		0.90	D
GERP RS		6.0
Varity_R		0.29
gMVP		0.71
Mutation Taster		=55/45	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

hg19: chrX-134030900; COSMIC: COSV66189140; COSMIC: COSV66189140;