Is KHK p.Asp295= (c.885T>C) pathogenic?

KHK p.Asp295= (c.885T>C) is classified Likely benign in KHK (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Rare (popmax 0.28%, afr); Associated with essential fructosuria.

What condition is associated with KHK p.Asp295= (c.885T>C)?

KHK p.Asp295= (c.885T>C) is associated with essential fructosuria (ClinVar).

How common is KHK p.Asp295= (c.885T>C) in the general population?

KHK p.Asp295= (c.885T>C) is rare (popmax 0.28%, afr) (gnomAD).

How is Essential fructosuria inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

KHK p.Asp295=

c.885T>C · rs144476131 · VCV896779

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.28%, afr)

Conditions

essential fructosuria

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -2.8	GERP -4.4
Overall
CADD	1.178	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.28% African / African-American · 210/75,048 alleles

Filtering AF 0.249% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.237%

Overall 0.0159% 257/1,614,054 alleles · rare exomes 111/1,461,808 · genomes 146/152,246 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.28%	357
Admixed American	0.055%	1,819
Remaining individualsnot grpmax-eligible	0.0176%	5,682
South Asian	0.0011%	91,066
European (non-Finnish)	0.000169%	589,981

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: KHK
Protein: p.Asp295=
Coding: c.885T>C
MANE Select: NM_006488
dbSNP: rs144476131
Type: single nucleotide variant
Location: chr2:27099738 (GRCh38)

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

Disease context

essential fructosuria — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Essential fructosuria (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages

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/khk-p-asp295 (accessed [today's date]).

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