HLA-DPA1 p.Met62Leu

Variant names:

• chr6-33069803-T-A
• NM_033554.4:c.184A>T
• HLA-DPA1 p.Met62Leu

Your query was ambiguous. Multiple possible variants found:

• chr6-33069803-T-A
• chr6-33069803-T-G
• chr6-33069801-CAT-TAA
• chr6-33069801-CAT-AAG
• chr6-33069801-CAT-GAG
• chr6-33069801-CAT-TAG

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_033554.4(HLA-DPA1):​c.184A>T​(p.Met62Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M62V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: HLA-DPA1 NM_033554.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58
• Publications: 0 publications found

Genes affected

HLA-DPA1 (HGNC:4938): (major histocompatibility complex, class II, DP alpha 1) HLA-DPA1 belongs to the HLA class II alpha chain paralogues. This class II molecule is a heterodimer consisting of an alpha (DPA) and a beta (DPB) chain, both anchored in the membrane. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. Class II molecules are expressed in antigen presenting cells (APC: B lymphocytes, dendritic cells, macrophages). The alpha chain is approximately 33-35 kDa and its gene contains 5 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, exon 4 encodes the transmembrane domain and the cytoplasmic tail. Within the DP molecule both the alpha chain and the beta chain contain the polymorphisms specifying the peptide binding specificities, resulting in up to 4 different molecules. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.015230715).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033554.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DPA1	NM_033554.4	MANE Select	c.184A>T	p.Met62Leu	missense	Exon 2 of 5	NP_291032.2
	HLA-DPA1	NM_001242524.2		c.184A>T	p.Met62Leu	missense	Exon 3 of 6	NP_001229453.1	P20036
	HLA-DPA1	NM_001242525.2		c.184A>T	p.Met62Leu	missense	Exon 3 of 6	NP_001229454.1	X5CKE2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-DPA1	ENST00000692443.1	MANE Select	c.184A>T	p.Met62Leu	missense	Exon 2 of 5	ENSP00000509163.1	P20036
	HLA-DPA1	ENST00000419277.5	TSL:6	c.184A>T	p.Met62Leu	missense	Exon 3 of 6	ENSP00000393566.1	P20036
	HLA-DPA1	ENST00000923943.1		c.184A>T	p.Met62Leu	missense	Exon 3 of 6	ENSP00000594002.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.0010
DANN	Benign	0.25
DEOGEN2	Benign	0.00051	T
Eigen	Benign	-2.2
Eigen_PC	Benign	-2.2
FATHMM_MKL	Benign	0.025	N
M_CAP	Benign	0.012	T
MetaRNN	Benign	0.015	T
MetaSVM	Benign	-0.90	T
MutationAssessor	Benign	0.015	N
PhyloP100		-2.6
PrimateAI	Benign	0.27	T
PROVEAN	Benign	-0.13	N
REVEL	Benign	0.067
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
Varity_R		0.24
gMVP		0.31
Mutation Taster		=98/2	polymorphism

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr6-33037580;