Is BTD p.Cys13= (c.39C>T) pathogenic?

BTD p.Cys13= (c.39C>T) is classified Likely benign in BTD (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-13). Ultra-rare (popmax 0.0624%, eas); Associated with biotinidase deficiency.

What condition is associated with BTD p.Cys13= (c.39C>T)?

BTD p.Cys13= (c.39C>T) is associated with biotinidase deficiency (ClinVar).

How common is BTD p.Cys13= (c.39C>T) in the general population?

BTD p.Cys13= (c.39C>T) is ultra-rare (popmax 0.0624%, eas) (gnomAD).

How is Biotinidase deficiency inherited?

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

BTD p.Cys13=

c.39C>T · rs201564216 · VCV24972

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0624%, eas)

Conditions

biotinidase deficiency

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 -7.1	GERP -1.2
Overall
CADD	6.032	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0624% East Asian · 28/44,888 alleles

Filtering AF 0.0443% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0382%

Overall 0.00675% 109/1,614,208 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0624%	1,603
Middle Eastern	0.0495%	2,021
South Asian	0.0406%	2,462
Remaining individualsnot grpmax-eligible	0.024%	4,167
African / African-American	0.00266%	37,527
European (non-Finnish)	0.00203%	49,168

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: BTD
Protein: p.Cys13=
Coding: c.39C>T
MANE Select: NM_001370658
dbSNP: rs201564216
Type: single nucleotide variant
Location: chr3:15635478 (GRCh38)
Gene constraint: LOEUF 1.22 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.77

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

Disease context

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

For Biotinidase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood, Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Worldwide)

Similar variants

BTD p.Cys13Phe Conflicting classifications of pathogenicity ★ ⚠ same residue
BTD p.Cys13fs Pathogenic ★★ same residue
BTD p.Cys13_Cys15delinsPheAla Pathogenic ★ same residue
BTD c.1330G>C Pathogenic ★★ same condition
BTD c.249+1G>T Likely pathogenic ★★ same condition
BTD c.400-2A>G Likely pathogenic ★★ same condition
BTD c.-17+2T>C Pathogenic/Likely pathogenic ★★ same condition
BTD p.Ala142Val Pathogenic/Likely pathogenic ★★ 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/btd-p-cys13 (accessed [today's date]).

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