Is KLF10 p.Pro259= (c.777A>C) pathogenic?

KLF10 p.Pro259= (c.777A>C) is classified Likely benign in KLF10 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-09). Absent from gnomAD v4.1; Associated with KLF10-related disorder.

What condition is associated with KLF10 p.Pro259= (c.777A>C)?

KLF10 p.Pro259= (c.777A>C) is associated with KLF10-related disorder (ClinVar).

How common is KLF10 p.Pro259= (c.777A>C) in the general population?

KLF10 p.Pro259= (c.777A>C) is absent from gnomAD v4.1 (gnomAD).

KLF10 p.Pro259=

c.777A>C · rs1587834203 · VCV3035444

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

KLF10-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.3	GERP -0.38
Overall
CADD	7.678	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: KLF10
Protein: p.Pro259=
Coding: c.777A>C
MANE Select: NM_005655
dbSNP: rs1587834203
Type: single nucleotide variant
Location: chr8:102651555 (GRCh38)
Gene constraint: LOEUF 0.817 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 50.62 · 1 PDB

Full KLF10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

KLF10-related disorder

Similar variants

KLF10 p.Ala355Ser Uncertain significance ★★ ⚠ same condition
KLF10 p.Pro336Leu Uncertain significance ★★ ⚠ same condition
KLF10 p.Ala111Val Uncertain significance ★★ ⚠ same type
KLF10 p.Ala113Pro Uncertain significance ★★ ⚠ same type
KLF10 p.Ala132Thr Uncertain significance ★★ ⚠ same type
KLF10 p.Ala203Ser Uncertain significance ★★ ⚠ same type
KLF10 p.Ala316Thr Uncertain significance ★★ ⚠ same type
KLF10 p.Ala354Val 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/klf10-p-pro259 (accessed [today's date]).

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