rs200302125

chr2-227307878-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PM1 PP3 BP4_Strong BS1_Supporting

The NM_000091.5(COL4A3):c.4421T>C(p.Leu1474Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0044 in 1,614,166 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.0024 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0046 (23 hom.)
• Consequence: COL4A3 NM_000091.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:4 U:13 B:7
• Conservation: PhyloP100: 7.67

Genes affected

COL4A3 (HGNC:2204): (collagen type IV alpha 3 chain) Type IV collagen, the major structural component of basement membranes, is a multimeric protein composed of 3 alpha subunits. These subunits are encoded by 6 different genes, alpha 1 through alpha 6, each of which can form a triple helix structure with 2 other subunits to form type IV collagen. This gene encodes alpha 3. In the Goodpasture syndrome, autoantibodies bind to the collagen molecules in the basement membranes of alveoli and glomeruli. The epitopes that elicit these autoantibodies are localized largely to the non-collagenous C-terminal domain of the protein. A specific kinase phosphorylates amino acids in this same C-terminal region and the expression of this kinase is upregulated during pathogenesis. This gene is also linked to an autosomal recessive form of Alport syndrome. The mutations contributing to this syndrome are also located within the exons that encode this C-terminal region. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter. [provided by RefSeq, Jun 2010]

MFF-DT (HGNC:41067): (MFF divergent transcript)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM1: In a domain Collagen IV NC1 (size 224) in uniprot entity CO4A3_HUMAN there are 39 pathogenic changes around while only 9 benign (81%) in NM_000091.5
• PP3: Multiple lines of computational evidence support a deleterious effect 9: AlphaMissense, BayesDel_addAF, BayesDel_noAF, Eigen, M_CAP, MutationAssessor, phyloP100way_vertebrate, PROVEAN, REVEL [when max_spliceai, FATHMM_MKL, MetaRNN, MutationTaster was below the threshold]
• BP4: Computational evidence support a benign effect (MetaRNN=0.038383782).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0046 (6724/1461862) while in subpopulation NFE AF= 0.00577 (6415/1111988). AF 95% confidence interval is 0.00565. There are 23 homozygotes in gnomad4_exome. There are 3231 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL4A3	NM_000091.5	c.4421T>C	p.Leu1474Pro	missense_variant	48/52	ENST00000396578.8
MFF-DT	NR_102371.1	n.48-2223A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL4A3	ENST00000396578.8	c.4421T>C	p.Leu1474Pro	missense_variant	48/52	1	NM_000091.5	P1
MFF-DT	ENST00000439598.6	n.48-2223A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.00244 AC: 372 AN: 152186 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000989

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00209

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000282

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00426

Gnomad OTH AF: 0.00287

GnomAD3 exomes AF: 0.00270 AC: 673 AN: 249412 Hom.: 0 AF XY: 0.00259 AC XY: 350 AN XY: 135304

Gnomad AFR exome AF: 0.000775

Gnomad AMR exome AF: 0.00217

Gnomad ASJ exome AF: 0.0000993

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000325

Gnomad NFE exome AF: 0.00502

Gnomad OTH exome AF: 0.00165

GnomAD4 exome AF: 0.00460 AC: 6724 AN: 1461862 Hom.: 23 Cov.: 32 AF XY: 0.00444 AC XY: 3231 AN XY: 727232

Gnomad4 AFR exome AF: 0.000717

Gnomad4 AMR exome AF: 0.00190

Gnomad4 ASJ exome AF: 0.0000383

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.000337

Gnomad4 NFE exome AF: 0.00577

Gnomad4 OTH exome AF: 0.00295

GnomAD4 genome AF: 0.00244 AC: 372 AN: 152304 Hom.: 0 Cov.: 32 AF XY: 0.00215 AC XY: 160 AN XY: 74478

Gnomad4 AFR AF: 0.000986

Gnomad4 AMR AF: 0.00209

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000282

Gnomad4 NFE AF: 0.00426

Gnomad4 OTH AF: 0.00284

Alfa AF: 0.00389 Hom.: 4

Bravo AF: 0.00267

TwinsUK AF: 0.00728 AC: 27

ALSPAC AF: 0.00571 AC: 22

ESP6500AA AF: 0.000793 AC: 3

ESP6500EA AF: 0.00414 AC: 34

ExAC AF: 0.00275 AC: 332

EpiCase AF: 0.00513

EpiControl AF: 0.00439

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:4 Uncertain:13 Benign:7

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:5 Benign:4

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Nov 06, 2023	Reported previously in association with COL4A3-related disorders and also reported as a polymorphism (PMID: 24130771, 25307543, 26346198, 12028435, 14871398); 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: 30819905, 14871398, 17216251, 31865346, 26809805, 24130771, 12028435, 7987301, 29924831, 9269635, 11044206, 31027891, 11961012, 14582039, 27932480, 21897443, 30406062, 25229338, 29271581, 28658201, 31903434, 33391746, 31256874, 26346198, 25307543, 30295827, 29204651, 31477057, 32887937, 34426522, 33040356, 32939031, 34013111, 33654185, 35602506, 35260866, 36134775, 11134255, 36100708, 35090027, 37163122, Venda2023[Abstract], 37895316, 37915894) -
Uncertain significance, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jan 17, 2020	- -
Likely benign, criteria provided, single submitter	clinical testing	Invitae	Jan 30, 2024	- -
Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Feb 22, 2023	- -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2024	COL4A3: PM3:Strong, PM2:Supporting -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jul 27, 2018	- -
Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -

Autosomal recessive Alport syndrome Pathogenic:2 Uncertain:4

Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins-Biomnis	Nov 01, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Mar 27, 2019	A heterozygous missense variant was identified, NM_000091.4(COL4A3):c.4421T>C in exon 48 of 52 of the COL4A3 gene. This substitution is predicted to create a moderate amino acid change from leucine to proline at position 1474 of the protein, NP_000082.2(COL4A3):p.(Leu1474Pro). The leucine at this position has very high conservation (100 vertebrates, UCSC), and is located within the C4 functional domain. In silico software predicts this variant to be pathogenic (PolyPhen, SIFT, CADD, MutationTaster). The variant is present in the gnomAD population database at a frequency of 0.27% (748 heterozygotes; 0 homozygotes). Previous reports of the pathogenicity of this variant are conflicting (ClinVar, Ottlewski, I. et al. (2019), Schapiro, D. et al. (2019)). Based on information available at the time of curation, this variant has been classified as a VARIANT of UNCERTAIN SIGNIFICANCE (VUS). NB: This variant has been reclassified to a VARIANT of UNCERTAIN SIGNIFICANCE (VUS) due to the reanalysis of published literature. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	Sep 18, 2023	PS3_Moderate, PM3_Strong, PP3 -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München	Apr 20, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Jul 14, 2022	- -

COL4A3-related disorder Pathogenic:1 Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Dec 17, 2018	The COL4A3 c.4421T>C (p.Leu1474Pro) variant has been reported in at least five studies and is found in a total of nine probands, including five probands with clinical symptoms of Alport syndrome, two of which are siblings, in a compound heterozygous state and four proband in a heterozygous state, including one sibling pair (Chatterjee et al. 2013; Nabais Sa et al. 2015; Gast et al. 2016; Bierzynska et al. 2017; Brandt et al. 2018). This included two compound heterozygous probands with end stage renal disease (Nabais Sa et al. 2015). The remaining three compound heterozygous probands were identified to have variants in additional genes known to be associated with glomerulopathy (Chatterjee et al. 2013; Gast et al. 2016). The c.4421T>C (p.Leu1474Pro) variant was also observed in a presumed heterozygous state in the unaffected brother of a compound heterozygote and this brother's son (Chatterjee et al. 2013). Control data are unavailable for this variant, which is reported at a frequency of 0.004899 in the European (non-Finnish) population of the Genome Aggregation Database. Based on the evidence, the p.Leu1474Pro variant is classified as likely pathogenic for COL4A3-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Uncertain significance, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Dec 16, 2023	The COL4A3 c.4421T>C variant is predicted to result in the amino acid substitution p.Leu1474Pro. In the compound heterozygous state with another pathogenic COL4A3 variant, the c.4421T>C (p.Leu1474Pro) variant has been reported in patients with autosomal recessive Alport syndrome or early progression to end-stage renal disease (Chatterjee et al. 2013. PubMed ID: 24130771; Gast et al. 2015. PubMed ID: 26346198; Nabais Sá et al. 2015. PubMed ID: 25307543; Boeckhaus et al. 2020. PubMed ID: 33040356). Of note, in the Chatterjee et al. study, the p.Leu1474Pro variant in the heterozygous state was also found in an unaffected brother and his son with unknown disease status. This variant in the heterozygous state has been repeatedly reported in patients with focal segmental glomerulosclerosis (Feltran et al. 2017. PubMed ID: 28658201; Gast et al. 2015. PubMed ID: 26346198; Malone et al. 2014. PubMed ID: 25229338). This variant was also reported in one patient with cervical artery dissection (Traenka et al. 2019. PubMed ID: 31903434). Furthermore, this variant along with a rare COL4A4 variant was reported in an identical twin brother-pair with cervical artery dissection (Brandt et al. 2018. PubMed ID: 29271581). This variant was reported in two siblings with IgA Nephropathy as variant of uncertain significance (Stapleton et al. 2020. PubMed ID: 31865346). However, the minor allele frequency of this variant in the general population reaches ~0.5%, which could be too high to be a primary cause of autosomal dominant COL4A3-related disease. Of note, incomplete penetrance has been reported in COL4A3-related disorders (Pescucci et al. 2004. PubMed ID: 15086897). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Autosomal dominant Alport syndrome Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Aug 10, 2023	Criteria applied: PP3 -
Uncertain significance, no assertion criteria provided	clinical testing	Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare	Jun 14, 2018	- -

Alport syndrome Uncertain:1 Benign:1

Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Jan 12, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill	Dec 11, 2020	- -

not specified Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Mar 30, 2022	Variant summary: COL4A3 c.4421T>C (p.Leu1474Pro) results in a non-conservative amino acid change located in the non-collagenous domain (IPR001442) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0027 in 249412 control chromosomes, predominantly at a frequency of 0.005 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 2.6-fold of the estimated maximal expected allele frequency for a pathogenic variant in COL4A3 causing Alport Syndrome, Autosomal Recessive phenotype (0.0019), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. The variant, c.4421T>C, has been reported in the literature in several individuals affected with Alport Syndrome, focal segmental glomerulosclerosis (FSGS), steroid-resistant nephrotic syndrome (SRNS) and other nephrotic phenotypes, however without strong evidence for causality (e.g. Lemmink_1994, VanDerLoop_2000, Heidet_2001, Vega_2003, Chatterjee_2013, Malone_2014, Gast_2016, Weber_2016, Bierzynska_2017, Lata_2018), several of these reports described the variant as polymorphism, and in some of the reported cases atypical findings for Alport Syndrome were noted, or co-occurring variants in COL4A3 (with dominant mode of inheritance) or other genes could potentially explain the phenotype. These reports do not provide unequivocal conclusions about association of the variant with Alport Syndrome, Autosomal Recessive. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Eighteen submitters have provided clinical-significance assessments for this variant in ClinVar after 2014, mostly without evidence for independent evaluation, and classified the variant with conflicting assessments, as pathogenic (n=1) / likely pathogenic (n=3), VUS (n=8), likely benign (n=4) / benign (n=2). Based on the evidence outlined above, the variant was classified as likely benign. -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jan 15, 2020	The p.Leu1474Pro variant in COL4A3 is classified as benign because it has been identified in 0.5% (627/128566) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). ACMG/AMP Criteria applied: BA1. -

Hearing impairment Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Department of Otolaryngology – Head & Neck Surgery, Cochlear Implant Center

Apr 12, 2021

PS1_Strong, PM2_Moderate, PP3_Supporting -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.94
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Pathogenic	0.55
Cadd	Uncertain	24
Dann	Uncertain	0.99
DEOGEN2	Uncertain	0.64	D;.
Eigen	Pathogenic	0.88
Eigen_PC	Pathogenic	0.78
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.91	D;D
M_CAP	Pathogenic	0.72	D
MetaRNN	Benign	0.038	T;T
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.7	H;.
MutationTaster	Benign	1.0	D
PrimateAI	Uncertain	0.67	T
PROVEAN	Pathogenic	-6.0	D;.
REVEL	Pathogenic	0.79
Sift	Pathogenic	0.0	D;.
Sift4G	Pathogenic	0.0	D;.
Polyphen		1.0	D;.
Vest4		0.98
MVP		0.97
MPC		0.30
ClinPred		0.088	T
GERP RS		5.9
Varity_R		0.96
gMVP		0.91

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: rs200302125; hg19: chr2-228172594;