Is UNC80 p.Ser3047= (c.9141C>T) pathogenic?

UNC80 p.Ser3047= (c.9141C>T) is classified Benign/Likely benign in UNC80 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-02). Rare (popmax 0.298%, nfe).

How common is UNC80 p.Ser3047= (c.9141C>T) in the general population?

UNC80 p.Ser3047= (c.9141C>T) is rare (popmax 0.298%, nfe) (gnomAD).

UNC80 p.Ser3047=

c.9141C>T · rs73003402 · VCV717614

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.298%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 3.5	GERP -0.75, phastCons 1
Overall
CADD	11.08	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.298% European (non-Finnish) · 3,422/1,146,878 alleles

Filtering AF 0.29% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.287%

Overall 0.247% 3,834/1,551,426 alleles · rare exomes 3,543/1,399,264 · genomes 291/152,162 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.436%	229
European (non-Finnish)grpmax	0.298%	335
Remaining individualsnot grpmax-eligible	0.183%	546
Finnishnot grpmax-eligible	0.167%	599
African / African-American	0.0424%	2,358
South Asian	0.0393%	2,546
Admixed American	0.0177%	5,665
Middle Eastern	0.0167%	5,988
East Asian	0.00734%	13,632

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: UNC80
Protein: p.Ser3047=
Coding: c.9141C>T
MANE Select: NM_001371986
dbSNP: rs73003402
Type: single nucleotide variant
Location: chr2:209982201 (GRCh38)
Gene constraint: LOEUF 0.48 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)

Full UNC80 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

UNC80 c.4110+1G>C Pathogenic/Likely pathogenic ★★ same type
UNC80 c.7287-1G>A Likely pathogenic ★★ same type
UNC80 c.8772+1G>A Likely pathogenic ★★ same type
UNC80 p.Arg1069Ter Pathogenic ★★ same type
UNC80 p.Arg1076Ter Pathogenic ★★ same type
UNC80 p.Arg1110Ter Pathogenic ★★ same type
UNC80 p.Arg1179Ter Pathogenic/Likely pathogenic ★★ same type
UNC80 p.Arg1285Ter Pathogenic ★★ same type

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/unc80-p-ser3047 (accessed [today's date]).

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