Is KBTBD13 p.Phe87= (c.261C>T) pathogenic?

KBTBD13 p.Phe87= (c.261C>T) is classified Likely benign in KBTBD13 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-18). Very rare (popmax 0.00816%, amr); Associated with nemaline myopathy 6.

What condition is associated with KBTBD13 p.Phe87= (c.261C>T)?

KBTBD13 p.Phe87= (c.261C>T) is associated with nemaline myopathy 6 (ClinVar).

How common is KBTBD13 p.Phe87= (c.261C>T) in the general population?

KBTBD13 p.Phe87= (c.261C>T) is very rare (popmax 0.00816%, amr) (gnomAD).

How is Childhood-onset nemaline myopathy inherited?

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

KBTBD13 p.Phe87=

c.261C>T · rs770172865 · VCV464352

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00816%, amr)

Conditions

nemaline myopathy 6

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 4.7	GERP 1.4, phastCons 1
Overall
CADD	13.06	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00816% Admixed American · 4/49,020 alleles

Filtering AF 0.0027% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00158%

Overall 0.00112% 17/1,515,474 alleles · very rare exomes 17/1,363,316 · genomes 0/152,158 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00816%	12,255
South Asian	0.00366%	27,330
European (non-Finnish)	0.000882%	113,400

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: KBTBD13
Protein: p.Phe87=
Coding: c.261C>T
MANE Select: NM_001101362
dbSNP: rs770172865
Type: single nucleotide variant
Location: chr15:65077076 (GRCh38)
Gene constraint: LOEUF 1.961 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.56

Full KBTBD13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

nemaline myopathy 6 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Childhood-onset nemaline myopathy (Orphanet):

Inheritance: Autosomal dominant
Onset: Childhood
Prevalence: <1 / 1 000 000 (Europe)

Similar variants

KBTBD13 p.Phe87Leu Uncertain significance ★ ⚠ same residue
KBTBD13 p.Lys390Asn Likely pathogenic ★★ ⚠ same condition
KBTBD13 p.Ala112Glu Uncertain significance ★★ same condition
KBTBD13 p.Ala192Glu Uncertain significance ★★ ⚠ same condition
KBTBD13 p.Ala262Thr Uncertain significance ★★ ⚠ same condition
KBTBD13 p.Ala301Ser Uncertain significance ★★ ⚠ same condition
KBTBD13 p.Ala324Thr Uncertain significance ★★ ⚠ same condition
KBTBD13 p.Ala396Val Uncertain significance ★★ ⚠ 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/kbtbd13-p-phe87 (accessed [today's date]).

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