Is EMD p.Ser171= (c.513A>G) pathogenic?

EMD p.Ser171= (c.513A>G) is classified Uncertain significance in EMD (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-31). Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with EMD p.Ser171= (c.513A>G)?

EMD p.Ser171= (c.513A>G) is associated with Cardiovascular phenotype (ClinVar).

How common is EMD p.Ser171= (c.513A>G) in the general population?

EMD p.Ser171= (c.513A>G) is absent from gnomAD v4.1 (gnomAD).

EMD p.Ser171=

c.513A>G · rs2522790231 · VCV2451682

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>T here scores Δ0.52 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.61	GERP -3.1, phastCons 0.27
Overall
CADD	10.9	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: EMD
Protein: p.Ser171=
Coding: c.513A>G
MANE Select: NM_000117
dbSNP: rs2522790231
Type: single nucleotide variant
Location: chrX:154380945 (GRCh38)
Structure: AlphaFold pLDDT 61.26 · 6 PDB
Residue 171: a modified residue (phosphoserine); the 'interaction with f-actin' region; the 'interaction with ctnnb1' region

Full EMD gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EMD p.Ser171Ter Pathogenic ★★ same residue
EMD c.400-3C>T Uncertain significance ★★ same condition
EMD c.449+4C>T Uncertain significance ★★ same condition
EMD p.Arg168Cys Uncertain significance ★★ ⚠ same condition
EMD p.Arg203His Uncertain significance ★★ ⚠ same condition
EMD p.Arg207Gln Uncertain significance ★★ ⚠ same condition
EMD p.Asp72Val Uncertain significance ★★ ⚠ same condition
EMD p.Glu146Lys Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/emd-p-ser171 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown