Is ESPNL p.Val843Met (c.2527G>A) pathogenic?

ESPNL p.Val843Met (c.2527G>A) is classified Uncertain significance in ESPNL (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-01). AlphaMissense: likely benign (0.1854); Rare (popmax 0.209%, nfe).

How common is ESPNL p.Val843Met (c.2527G>A) in the general population?

ESPNL p.Val843Met (c.2527G>A) is rare (popmax 0.209%, nfe) (gnomAD).

What do computational predictors say about ESPNL p.Val843Met (c.2527G>A)?

AlphaMissense predicts likely benign (score 0.1854) — an in-silico prediction, not a clinical call.

ESPNL p.Val843Met

c.2527G>A · rs201231172 · VCV2381752

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1854 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.209%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1854	likely benign
REVEL	0.16	moderately benign-leaning
SaProt	LLR -8.10	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.3	GERP -0.6, phastCons 1
Regional constraint	o/e 1.07	unconstrained · MANE · 31 kb · p 0.0064 · regional, not allelic
Overall
CADD	22.6	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.209% European (non-Finnish) · 2,421/1,158,124 alleles

Filtering AF 0.202% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.199%

Overall 0.169% 2,642/1,565,150 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.209%	478
Remaining individualsnot grpmax-eligible	0.166%	601
Admixed American	0.143%	697
African / African-American	0.0378%	2,643
Ashkenazi Jewishnot grpmax-eligible	0.0208%	4,798
Finnishnot grpmax-eligible	0.0146%	6,866
South Asian	0.00117%	85,594

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ESPNL
Protein: p.Val843Met
Coding: c.2527G>A
MANE Select: NM_194312
dbSNP: rs201231172
Type: single nucleotide variant
Location: chr2:238131241 (GRCh38)
Gene constraint: LOEUF 1.651 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 65.57

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

Similar variants

ESPNL p.Arg167Gln Benign ★★ same type
ESPNL p.Arg351Cys Benign ★★ ⚠ same type
ESPNL c.672+1G>A Uncertain significance ★ same type
ESPNL p.Ala112Ser Uncertain significance ★ ⚠ same type
ESPNL p.Ala144Asp Uncertain significance ★ ⚠ same type
ESPNL p.Ala144Thr Uncertain significance ★ ⚠ same type
ESPNL p.Ala145Thr Uncertain significance ★ ⚠ same type
ESPNL p.Ala159Thr Uncertain significance ★ ⚠ same type

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/espnl-p-val843met (accessed [today's date]).

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