rs200302125

Variant names:

• chr2-227307878-T-C
• rs200302125
• NM_000091.5:c.4421T>C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 3P and 9B. PM1 PP3 BP4_Strong BS1_Supporting BS2

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:5 U:14 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 -6 ACMG points.

• PM1: In a chain Tumstatin (size 244) in uniprot entity CO4A3_HUMAN there are 24 pathogenic changes around while only 2 benign (92%) 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 allele frequency = 0.00244 (372/152304) while in subpopulation NFE AF= 0.00426 (290/68014). AF 95% confidence interval is 0.00386. There are 0 homozygotes in gnomad4. There are 160 alleles in male gnomad4 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
• BS2: High Homozygotes in GnomAdExome4 at 23 SD gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL4A3	NM_000091.5	c.4421T>C	p.Leu1474Pro	missense_variant	Exon 48 of 52	ENST00000396578.8	NP_000082.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL4A3	ENST00000396578.8	c.4421T>C	p.Leu1474Pro	missense_variant	Exon 48 of 52	1	NM_000091.5	ENSP00000379823.3

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:5 Uncertain:14 Benign:7

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:6 Benign:4

-

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jan 16, 2025

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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, 36117978, 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, 38740443) -

-

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Dec 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

COL4A3: PM3:Strong, PM2:Supporting -

-

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jul 27, 2018

Eurofins Ntd Llc (ga)

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 17, 2020

Athena Diagnostics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 21, 2024

Mayo Clinic Laboratories, Mayo Clinic

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PP3, PM3 -

Feb 22, 2023

Revvity Omics, Revvity

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Autosomal recessive Alport syndrome Pathogenic:2 Uncertain:3

Jul 14, 2022

MGZ Medical Genetics Center

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 20, 2020

Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 01, 2022

Eurofins-Biomnis

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 18, 2023

Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PS3_Moderate, PM3_Strong, PP3 -

May 28, 2019

Mendelics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Autosomal dominant Alport syndrome Pathogenic:1 Uncertain:2

Aug 10, 2023

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Criteria applied: PP3 -

May 01, 2024

Laboratory of Prof. Karen Avraham, Tel Aviv University

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

Pathogenic by Deafness Variation Database and by ClinVar based on PMID: 31477057. -

Jun 14, 2018

Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Alport syndrome Uncertain:2 Benign:1

Jan 12, 2020

Natera, Inc.

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jun 24, 2022

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3B. Following criteria are met: 0103 - Dominant negative and loss of function are known mechanisms of disease in this gene and are associated with COL4A3-related nephropathy. Glycine changes that are part of a G-X-Y repeat in the triple helix of a collagen domain are known to have a dominant negative effect (PMID: 12028435). (I) 0108 - This gene is associated with both recessive (Alport syndrome 2 MIM#203780) and dominant disease (Alport syndrome 3 MIM#104200 and benign familial hematuria MIM#141200) (OMIM). (I) 0200 - Variant is predicted to result in a missense amino acid change from leucine to proline. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (748 heterozygotes, 0 homozygotes). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated C4 domain (NCBI). (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0808 - Previous reports of pathogenicity for this variant are conflicting. This variant has been reported with conflicting classifications from benign to pathogenic. Although this variant has been reported in both heterozygous and compound heterozygous states in multiple patients with renal conditions, there is still uncertainty surrounding its contribution to disease (ClinVar, LOVD, Decipher, PMID: 31477057, 32887937). (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Dec 11, 2020

UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

COL4A3-related disorder Pathogenic:1 Uncertain:1

Jun 07, 2024

PreventionGenetics, part of Exact Sciences

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

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. -

Dec 17, 2018

Illumina Laboratory Services, Illumina

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

not specified Benign:2

Jan 15, 2020

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Mar 30, 2022

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Hearing impairment Pathogenic:1

Apr 12, 2021

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

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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;.
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;