Is BEND7 p.Ser438Leu (c.1313C>T) pathogenic?

BEND7 p.Ser438Leu (c.1313C>T) is classified Uncertain significance in BEND7 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-23). Very rare (popmax 0.00223%, eas).

How common is BEND7 p.Ser438Leu (c.1313C>T) in the general population?

BEND7 p.Ser438Leu (c.1313C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

BEND7 p.Ser438Leu

c.1313C>T · VCV4645774

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.04	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.2	GERP -0.077, phastCons 0.001
Overall
CADD	7.16	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,900 alleles

Filtering AF 0.000365% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000136%

Overall 0.000248% 4/1,614,112 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,900
South Asian	0.0022%	45,546
European (non-Finnish)	8.47e-05%	1,180,044

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: BEND7
Protein: p.Ser438Leu
Coding: c.1313C>T
MANE Select: NM_001369863 · reported on NM_152751
Type: single nucleotide variant
Location: chr10:13439266 (GRCh38)
Gene constraint: LOEUF 0.842 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 62.17

Full BEND7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BEND7 p.Ala103Val Uncertain significance ★ same type
BEND7 p.Ala105Asp Uncertain significance ★ same type
BEND7 p.Ala105Val Uncertain significance ★ same type
BEND7 p.Ala255Gly Uncertain significance ★ same type
BEND7 p.Ala397Val Uncertain significance ★ same type
BEND7 p.Arg114Cys Uncertain significance ★ same type
BEND7 p.Arg134Cys Uncertain significance ★ same type
BEND7 p.Arg136Gly 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/bend7-p-ser438leu (accessed [today's date]).

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