Is BEND2 p.Glu196Lys (c.586G>A) pathogenic?

BEND2 p.Glu196Lys (c.586G>A) is classified Likely benign in BEND2 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-05-21). AlphaMissense: likely benign (0.0803); Rare (popmax 0.593%, nfe).

How common is BEND2 p.Glu196Lys (c.586G>A) in the general population?

BEND2 p.Glu196Lys (c.586G>A) is rare (popmax 0.593%, nfe) (gnomAD).

What do computational predictors say about BEND2 p.Glu196Lys (c.586G>A)?

AlphaMissense predicts likely benign (score 0.0803) — an in-silico prediction, not a clinical call.

BEND2 p.Glu196Lys

c.586G>A · rs147763153 · VCV788157

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0803 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.593%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0803	likely benign
REVEL	0.012	strongly benign-leaning
SaProt	LLR -6.57	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 1.2	GERP -1.3, phastCons 0.001
Regional constraint	o/e 1.00	unconstrained · MANE · 50 kb · p 0.98 · regional, not allelic
Overall
CADD	4.263	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.593% European (non-Finnish) · 5,304/894,216 alleles

Filtering AF 0.58% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.574%

Overall 0.472% 5,705/1,209,348 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.593%	169
Remaining individualsnot grpmax-eligible	0.353%	283
Finnishnot grpmax-eligible	0.201%	496
Middle Eastern	0.184%	543
South Asian	0.104%	963
African / African-American	0.0819%	1,222
Ashkenazi Jewishnot grpmax-eligible	0.0363%	2,753
Admixed American	0.0284%	3,524
East Asian	0.0118%	8,442

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: BEND2
Protein: p.Glu196Lys
Coding: c.586G>A
MANE Select: NM_153346
dbSNP: rs147763153
Type: single nucleotide variant
Location: chrX:18203822 (GRCh38)
Structure: AlphaFold pLDDT 49.94

Full BEND2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BEND2 p.Gln198His Benign ★★ same type
BEND2 p.Gly580Val Benign ★★ same type
BEND2 p.Ser183Ile Benign ★★ ⚠ same type
BEND2 p.Thr367= Likely benign ★★ same type
BEND2 p.Val261Gly Benign ★★ same type
BEND2 p.Ala185Gly Uncertain significance ★ ⚠ same type
BEND2 p.Ala193Thr Uncertain significance ★ ⚠ same type
BEND2 p.Ala222Ser 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/bend2-p-glu196lys (accessed [today's date]).

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