Is KRT83 p.Cys446= (c.1338C>T) pathogenic?

KRT83 p.Cys446= (c.1338C>T) is classified Benign/Likely benign in KRT83 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-12-25). Rare (popmax 0.952%, afr); Associated with monilethrix.

What condition is associated with KRT83 p.Cys446= (c.1338C>T)?

KRT83 p.Cys446= (c.1338C>T) is associated with monilethrix (ClinVar).

How common is KRT83 p.Cys446= (c.1338C>T) in the general population?

KRT83 p.Cys446= (c.1338C>T) is rare (popmax 0.952%, afr) (gnomAD).

How is Monilethrix inherited?

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

KRT83 p.Cys446=

c.1338C>T · rs11836080 · VCV309498

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.952%, afr)

Conditions

monilethrix

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.28 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.88	GERP -3.7
Overall
CADD	2.436	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.952% African / African-American · 713/74,934 alleles

Filtering AF 0.894% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.87%

Overall 0.129% 2,066/1,606,264 alleles · rare exomes 1,608/1,453,946 · genomes 458/152,318 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.952%	105
South Asian	0.682%	147
Ashkenazi Jewishnot grpmax-eligible	0.422%	237
Middle Eastern	0.318%	315
Remaining individualsnot grpmax-eligible	0.158%	634
Admixed American	0.142%	707
European (non-Finnish)	0.0357%	2,803
East Asian	0.00448%	22,326
Finnishnot grpmax-eligible	0.00158%	63,452

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: KRT83
Protein: p.Cys446=
Coding: c.1338C>T
MANE Select: NM_002282
dbSNP: rs11836080
Type: single nucleotide variant
Location: chr12:52314775 (GRCh38)
Gene constraint: LOEUF 1.226 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.81
Residue 446: the 'tail' region

Full KRT83 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

For Monilethrix (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

KRT83 p.Cys446Tyr Uncertain significance ★ ⚠ same residue
KRT83 p.Glu407Lys Likely pathogenic ★★ same condition
KRT83 p.Arg168Trp Uncertain significance ★★ ⚠ same condition
KRT83 p.Arg272Gln Uncertain significance ★★ ⚠ same condition
KRT83 p.Glu172Lys Uncertain significance ★★ ⚠ same condition
KRT83 c.1041+6A>G Benign ★★ same condition
KRT83 c.1042-4C>A Benign ★★ same condition
KRT83 c.750+15A>G Benign ★★ same condition

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/krt83-p-cys446 (accessed [today's date]).

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