rs3213451

Positions:

• chrX-21843316-A-C
• chrX-21843316-A-G
• chrX-21843316-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The ENST00000379484.10(MBTPS2):​c.222A>C​(p.Gln74His) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. Q74Q) has been classified as Benign.

• Frequency: Genomes: not found (cov: 23)
• Consequence: MBTPS2 ENST00000379484.10 missense, splice_region
• Scores: Splicing: ADA: 0.0003410
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

Genes affected

MBTPS2 (HGNC:15455): (membrane bound transcription factor peptidase, site 2) This gene encodes a intramembrane zinc metalloprotease, which is essential in development. This protease functions in the signal protein activation involved in sterol control of transcription and the ER stress response. Mutations in this gene have been associated with ichthyosis follicularis with atrichia and photophobia (IFAP syndrome); IFAP syndrome has been quantitatively linked to a reduction in cholesterol homeostasis and ER stress response.[provided by RefSeq, Aug 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.28873354).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MBTPS2	NM_015884.4	c.222A>C	p.Gln74His	missense_variant, splice_region_variant	2/11	ENST00000379484.10	NP_056968.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MBTPS2	ENST00000379484.10	c.222A>C	p.Gln74His	missense_variant, splice_region_variant	2/11	1	NM_015884.4	ENSP00000368798	P1
MBTPS2	ENST00000365779.2	c.222A>C	p.Gln74His	missense_variant, splice_region_variant	2/7	1		ENSP00000368796
MBTPS2	ENST00000465888.1	n.321A>C		splice_region_variant, non_coding_transcript_exon_variant	2/6	2

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Uncertain	0.021	T
BayesDel_noAF	Benign	-0.21
CADD	Benign	9.3
DANN	Benign	0.96
DEOGEN2	Benign	0.043	T;T
FATHMM_MKL	Benign	0.53	D
LIST_S2	Uncertain	0.86	D;D
M_CAP	Uncertain	0.15	D
MetaRNN	Benign	0.29	T;T
MetaSVM	Uncertain	-0.088	T
MutationAssessor	Benign	1.6	L;.
MutationTaster	Benign	0.98	P;P
PrimateAI	Uncertain	0.54	T
PROVEAN	Benign	-0.85	N;N
REVEL	Uncertain	0.38
Sift	Uncertain	0.021	D;T
Sift4G	Uncertain	0.020	D;D
Polyphen		0.83	P;P
Vest4		0.37
MutPred		0.41		Loss of MoRF binding (P = 0.0958);Loss of MoRF binding (P = 0.0958);
MVP		0.75
MPC		0.62
ClinPred		0.24	T
GERP RS		-3.5
Varity_R		0.16
gMVP		0.59

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00034
dbscSNV1_RF	Benign	0.076
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs3213451; hg19: chrX-21861434;