rs121434287

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2PP5_Very_Strong

The NM_130849.4(SLC39A4):c.599C>T(p.Pro200Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,613,194 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. P200P) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.00014 ( 0 hom., cov: 33)

Exomes 𝑓: 0.00018 ( 0 hom. )

Consequence

SLC39A4
NM_130849.4 missense

Scores

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:6

Conservation

PhyloP100: 1.72

Variant links:

Genes affected

SLC39A4 (HGNC:17129): (solute carrier family 39 member 4) This gene encodes a member of the zinc/iron-regulated transporter-like protein (ZIP) family. The encoded protein localizes to cell membranes and is required for zinc uptake in the intestine. Mutations in this gene result in acrodermatitis enteropathica. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2013]

SLC39A4 links:

LOC124902041 (HGNC:):

LOC124902041 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 10 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 8-144415295-G-A is Pathogenic according to our data. Variant chr8-144415295-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 3537.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-144415295-G-A is described in Lovd as [Likely_pathogenic]. Variant chr8-144415295-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC39A4	NM_130849.4 linkuse as main transcript	c.599C>T	p.Pro200Leu	missense_variant	3/12	ENST00000301305.8
LOC124902041	XR_007061145.1 linkuse as main transcript	n.764G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A4	ENST00000301305.8 linkuse as main transcript	c.599C>T	p.Pro200Leu	missense_variant	3/12	1	NM_130849.4	P1	Q6P5W5-1
SLC39A4	ENST00000276833.9 linkuse as main transcript	c.524C>T	p.Pro175Leu	missense_variant	2/11	2			Q6P5W5-2
SLC39A4	ENST00000526658.1 linkuse as main transcript	c.317C>T	p.Pro106Leu	missense_variant	2/4	3

Frequencies

GnomAD3 genomes

AF:

0.000145

AC:

AN:

152156

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000654

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.000282

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000221

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.000128

AC:

AN:

249864

Hom.:

AF XY:

0.000140

AC XY:

AN XY:

135524

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000116

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0000926

Gnomad NFE exome

AF:

0.000195

Gnomad OTH exome

AF:

0.000164

GnomAD4 exome

AF:

0.000181

AC:

264

AN:

1460920

Hom.:

Cov.:

AF XY:

0.000180

AC XY:

131

AN XY:

726776

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000112

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0000232

Gnomad4 FIN exome

AF:

0.0000949

Gnomad4 NFE exome

AF:

0.000220

Gnomad4 OTH exome

AF:

0.0000828

GnomAD4 genome

AF:

0.000144

AC:

AN:

152274

Hom.:

Cov.:

AF XY:

0.000175

AC XY:

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.0000654

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.000282

Gnomad4 NFE

AF:

0.000221

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.000139

Hom.:

Bravo

AF:

0.000106

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000116

AC:

ExAC

AF:

0.000132

AC:

EpiCase

AF:

0.00

EpiControl

AF:

0.000178

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 04, 2024	This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 200 of the SLC39A4 protein (p.Pro200Leu). This variant is present in population databases (rs121434287, gnomAD 0.02%). This missense change has been observed in individual(s) with acrodermatitis enteropathica (PMID: 12068297, 12955721). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 3537). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects SLC39A4 function (PMID: 14709598, 31979155). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 16, 2023	Functional studies indicate P200L affects the uptake of zinc and suggests the function of the protein may be impaired, with the availability of the protein at the plasma membrane also affected (Wang et al., 2004; Kambe et al., 2009); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 19370757, 17483098, 27321477, 12068297, 18936158, 16819703, 28717982, 31979155, 33837739, 31589614, 33889411, 12955721, 14709598) -

Hereditary acrodermatitis enteropathica

Pathogenic:2

Pathogenic, no assertion criteria provided	literature only	OMIM	Jul 01, 2002	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Jan 14, 2022	- -

SLC39A4-related disorder

Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 26, 2023

The SLC39A4 c.599C>T variant is predicted to result in the amino acid substitution p.Pro200Leu. This variant was reported in the homozygous and compound heterozygous states in individuals with acrodermatitis enteropathica, including in multiple affected individuals from the same family (Families E and F, Kury et al. 2002. PubMed ID: 12068297; Families E and F previously reported by this group and Patient S-28, Kury et al. 2003. PubMed ID: 12955721; Patient previously reported by this group as Patient S-28, Lehnert et al. 2006. PubMed ID: 16819703). Functional studies in mouse models showed that this variant lead to wild-type levels of protein accumulation, however it was associated with increased accumulation of smaller molecular mass forms of protein (Wang et al. 2004. PubMed ID: 14709598). Additional studies in mouse models also showed that this variant had a modest impact on protein function and was overall similar to that of wild-type function (Wang et al. 2004. PubMed ID: 14709598). Additional functional studies using human embryonic kidney cells have conflicting results on the impact of the p.Pro200Leu variant on protein function (Hoch and Hershfinkel. 2020. PubMed ID: 31979155; Kuliyev and Sui. 2021. PubMed ID: 33837739). This variant is reported in 0.020% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/8-145640679-G-A) and is interpreted as likely pathogenic by several outside laboratories in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/3537/). Taken together, we interpret this variant as likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.57

BayesDel_addAF

Benign

-0.064

BayesDel_noAF

Uncertain

-0.040

Cadd

Pathogenic

Dann

Uncertain

1.0

Eigen

Uncertain

0.33

Eigen_PC

Uncertain

0.29

FATHMM_MKL

Benign

0.76

LIST_S2

Benign

0.85

T;T;T

M_CAP

Pathogenic

0.63

MetaRNN

Uncertain

0.60

D;D;D

MetaSVM

Benign

-0.47

MutationTaster

Benign

1.0

A;A

PrimateAI

Uncertain

0.72

PROVEAN

Pathogenic

-7.5

D;D;D

REVEL

Uncertain

0.40

Sift

Pathogenic

0.0

D;D;D

Sift4G

Pathogenic

0.0

D;D;.

Polyphen

1.0

.;D;.

Vest4

0.63

MVP

0.77

MPC

0.60

ClinPred

0.43

GERP RS

5.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.19

gMVP

0.66

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over