chr1-28993490-T-C

Variant names:

• chr1-28993490-T-C
• rs121434564
• ENST00000373800.7:c.2T>C

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PVS1 PS1_Moderate PM2 PP5

The NM_001376022.1(EPB41):​c.2T>C​(p.Met1?) variant causes a start lost change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: EPB41 NM_001376022.1 start_lost
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 6.61

Genes affected

EPB41 (HGNC:3377): (erythrocyte membrane protein band 4.1) The protein encoded by this gene, together with spectrin and actin, constitute the red cell membrane cytoskeletal network. This complex plays a critical role in erythrocyte shape and deformability. Mutations in this gene are associated with type 1 elliptocytosis (EL1). Alternatively spliced transcript variants encoding different isoforms have been described for this gene.[provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Pathogenic. Variant got 13 ACMG points.

• PVS1: Start lost variant, next in-frame start position is after 10 pathogenic variants. Next in-frame start position is after 159 codons. Genomic position: 29018420. Lost 0.241 part of the original CDS.
• PS1: Another start lost variant in NM_001376022.1 (EPB41) was described as [Pathogenic] in ClinVar as 16714
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 1-28993490-T-C is Pathogenic according to our data. Variant chr1-28993490-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 16715.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPB41	NM_001376013.1	c.629T>C	p.Met210Thr	missense_variant	Exon 3 of 21	ENST00000343067.9	NP_001362942.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPB41	ENST00000343067.9	c.629T>C	p.Met210Thr	missense_variant	Exon 3 of 21	5	NM_001376013.1	ENSP00000345259.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Elliptocytosis 1 Pathogenic:1

Jan 01, 1995

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.68
BayesDel_addAF	Pathogenic	0.41	D
BayesDel_noAF	Pathogenic	0.35
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.74	.;.;D;T;.;.;.;.;.;.;.;D;.;.;.;.;.;.;.
Eigen	Uncertain	0.39
Eigen_PC	Uncertain	0.45
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Uncertain	0.90	D;D;D;D;D;D;D;D;D;D;D;.;D;D;D;D;D;D;D
M_CAP	Uncertain	0.17	D
MetaRNN	Pathogenic	0.80	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	-0.093	T
MutationAssessor	Benign	1.7	.;.;L;.;.;.;.;.;.;L;.;L;.;.;.;.;L;.;.
PrimateAI	Uncertain	0.60	T
PROVEAN	Uncertain	-4.0	.;.;D;N;.;.;.;D;.;D;.;D;.;.;.;.;D;.;.
REVEL	Pathogenic	0.69
Sift	Benign	0.055	.;.;T;D;.;.;.;D;.;D;.;T;.;.;.;.;D;.;.
Sift4G	Benign	0.062	.;.;T;D;.;.;.;D;.;T;.;T;.;.;.;.;T;.;.
Polyphen		0.85	P;.;B;.;.;.;.;P;.;B;.;B;.;.;.;.;P;.;.
Vest4		0.84, 0.85, 0.84, 0.84, 0.86
MutPred		0.48		.;.;Loss of catalytic residue at M210 (P = 5e-04);.;.;.;.;.;.;Loss of catalytic residue at M210 (P = 5e-04);Loss of catalytic residue at M210 (P = 5e-04);Loss of catalytic residue at M210 (P = 5e-04);Loss of catalytic residue at M210 (P = 5e-04);Loss of catalytic residue at M210 (P = 5e-04);Loss of catalytic residue at M210 (P = 5e-04);Loss of catalytic residue at M210 (P = 5e-04);Loss of catalytic residue at M210 (P = 5e-04);Loss of catalytic residue at M210 (P = 5e-04);Loss of catalytic residue at M210 (P = 5e-04);
MVP		0.95
MPC		0.83
ClinPred		0.99	D
GERP RS		5.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.71
gMVP		0.62

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

Publications

LitVar

Other links and lift over

dbSNP: rs121434564; hg19: chr1-29320002;