NM_000091.5(COL4A3):c.222G>T (p.Pro74=) AND Alport syndrome

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Apr 27, 2017
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001138281.7

Allele description [Variation Report for NM_000091.5(COL4A3):c.222G>T (p.Pro74=)]

NM_000091.5(COL4A3):c.222G>T (p.Pro74=)

Genes:

MFF-DT:MFF divergent transcript [Gene - HGNC]
COL4A3:collagen type IV alpha 3 chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q36.3

Genomic location:

Preferred name:

NM_000091.5(COL4A3):c.222G>T (p.Pro74=)

HGVS:

NC_000002.12:g.227240220G>T
NG_011591.1:g.80656G>T
NM_000091.5:c.222G>TMANE SELECT
NP_000082.2:p.Pro74=
NP_000082.2:p.Pro74=
LRG_230t1:c.222G>T
LRG_230:g.80656G>T
LRG_230p1:p.Pro74=
NC_000002.11:g.228104936G>T
NM_000091.3:c.222G>T
NM_000091.4:c.222G>T

Links:

dbSNP: rs187950806

NCBI 1000 Genomes Browser:

rs187950806

Molecular consequence:

NM_000091.5:c.222G>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Alport syndrome
Synonyms:: Hemorrhagic familial nephritis; Hemorrhagic hereditary nephritis; Congenital hereditary hematuria
Identifiers:: MONDO: MONDO:0018965; MedGen: C1567741; OMIM: PS301050

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001298322	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 14582039, 17216251 Citation Link,
SCV002076374	Natera, Inc.	no assertion criteria provided	Benign (Dec 3, 2019)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001298322

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV002076374

Natera, Inc.

no assertion criteria provided

Benign
(Dec 3, 2019)

germline

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Autosomal recessive Alport's syndrome and benign familial hematuria are collagen type IV diseases.

Tazón Vega B, Badenas C, Ars E, Lens X, Milà M, Darnell A, Torra R.

Am J Kidney Dis. 2003 Nov;42(5):952-9.

PubMed [citation]

PMID:: 14582039

Nine novel COL4A3 and COL4A4 mutations and polymorphisms identified in inherited membrane diseases.

Rana K, Tonna S, Wang YY, Sin L, Lin T, Shaw E, Mookerjee I, Savige J.

Pediatr Nephrol. 2007 May;22(5):652-7. Epub 2007 Jan 10.

PubMed [citation]

PMID:: 17216251

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001298322.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Natera, Inc., SCV002076374.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 20, 2025

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