Is KLF1 p.Pro59= (c.177C>T) pathogenic?

KLF1 p.Pro59= (c.177C>T) is classified Likely benign in KLF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-17). No allele count reported in gnomAD v4.1 (AN 1,610,630).

How common is KLF1 p.Pro59= (c.177C>T) in the general population?

KLF1 p.Pro59= (c.177C>T) is no allele count reported in gnomAD v4.1 (AN 1,610,630) (gnomAD).

KLF1 p.Pro59=

c.177C>T · rs915605127 · VCV2713811

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,610,630)

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 -2.1	GERP -2.7
Overall
CADD	1.316	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,610,630). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: KLF1
Protein: p.Pro59=
Coding: c.177C>T
MANE Select: NM_006563
dbSNP: rs915605127
Type: single nucleotide variant
Location: chr19:12886053 (GRCh38)
Gene constraint: LOEUF 1.777 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 58.11 · 3 PDB
Residue 59: a UniProt-annotated variant site (in cdan4b; likely pathogenic); the 'disordered' region

Full KLF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

KLF1 p.Ala298Pro Pathogenic ★★ same type
KLF1 c.*263C>T Uncertain significance ★★ same type
KLF1 p.Ala142Val Uncertain significance ★★ ⚠ same type
KLF1 p.Ala165Ser Uncertain significance ★★ ⚠ same type
KLF1 p.Ala262Ser Uncertain significance ★★ ⚠ same type
KLF1 p.Arg137Cys Uncertain significance ★★ ⚠ same type
KLF1 p.Arg328His Uncertain significance ★★ ⚠ same type
KLF1 p.Arg340His 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/klf1-p-pro59 (accessed [today's date]).

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