Is TYR p.Ser16= (c.48C>T) pathogenic?

TYR p.Ser16= (c.48C>T) is classified Likely benign in TYR (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-06-11). Ultra-rare (popmax 0.0981%, eas); Associated with oculocutaneous albinism type 1A.

What condition is associated with TYR p.Ser16= (c.48C>T)?

TYR p.Ser16= (c.48C>T) is associated with oculocutaneous albinism type 1A, oculocutaneous albinism type 1B (ClinVar).

How common is TYR p.Ser16= (c.48C>T) in the general population?

TYR p.Ser16= (c.48C>T) is ultra-rare (popmax 0.0981%, eas) (gnomAD).

How is Oculocutaneous albinism type 1 inherited?

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

TYR p.Ser16=

c.48C>T · rs148710429 · VCV1596806

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0981%, eas)

Conditions

oculocutaneous albinism type 1A

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 -6.3	GERP -3.8
Overall
CADD	1.339	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0981% East Asian · 44/44,872 alleles

Filtering AF 0.075% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0669%

Overall 0.00533% 86/1,614,132 alleles · ultra-rare exomes 73/1,461,866 · genomes 13/152,266 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0981%	1,020
South Asian	0.00549%	18,214
European (non-Finnish)	0.0028%	35,758
African / African-American	0.00267%	37,522
Admixed American	0.00167%	60,020
Remaining individualsnot grpmax-eligible	0.0016%	62,508

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: TYR
Protein: p.Ser16=
Coding: c.48C>T
MANE Select: NM_000372
dbSNP: rs148710429
Type: single nucleotide variant
Location: chr11:89178001 (GRCh38)
Gene constraint: LOEUF 1.346 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.79 · 1 PDB

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

Disease context

oculocutaneous albinism type 1A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: oculocutaneous albinism type 1B

For Oculocutaneous albinism type 1 (Orphanet):

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

Similar variants

TYR c.1036+1G>A Pathogenic/Likely pathogenic ★★ same condition
TYR c.1036+2T>G Pathogenic ★★ same condition
TYR c.1037-1G>A Pathogenic/Likely pathogenic ★★ same condition
TYR c.1037-2A>G Pathogenic/Likely pathogenic ★★ same condition
TYR c.1037-3C>G Pathogenic/Likely pathogenic ★★ same condition
TYR c.1037-7T>A Pathogenic/Likely pathogenic ★★ same condition
TYR c.1185-2A>G Pathogenic/Likely pathogenic ★★ same condition
TYR c.1366+1G>T 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/tyr-p-ser16 (accessed [today's date]).

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