CTU2 p.Arg501=

Q: Is CTU2 p.Arg501= (c.1503G>C) pathogenic?

CTU2 p.Arg501= (c.1503G>C) is classified Benign in CTU2 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-01). Common (popmax 31.7%, mid) — too common for a highly-penetrant pathogenic allele; Associated with microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome.

Q: What condition is associated with CTU2 p.Arg501= (c.1503G>C)?

CTU2 p.Arg501= (c.1503G>C) is associated with microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome (ClinVar).

Q: How common is CTU2 p.Arg501= (c.1503G>C) in the general population?

CTU2 p.Arg501= (c.1503G>C) is common (popmax 31.7%, mid) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1503G>C · rs1058158 · VCV1255421

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 31.7%, mid) — too common for a highly-penetrant pathogenic allele

Conditions

microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.008	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.1	GERP -2.6, phastCons 0.47
Overall
CADD	1.689	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 31.7% Middle Eastern · 1,917/6,052 alleles

Filtering AF 31.2% ClinGen BA1/BS1 input FAF95, joint · FAF99 31.1%

Overall 28.8% 463,590/1,611,996 alleles · common exomes 427,013/1,459,920 · genomes 36,577/152,076 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	31.7%	3
South Asian	31.5%	3
European (non-Finnish)	31.1%	3
Ashkenazi Jewishnot grpmax-eligible	31%	3
Amishnot grpmax-eligible	30.1%	3
Remaining individualsnot grpmax-eligible	27.8%	4
Finnishnot grpmax-eligible	25.8%	4
Admixed American	15.6%	6
African / African-American	13.7%	7
East Asian	8.37%	12

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: CTU2
Protein: p.Arg501=
Coding: c.1503G>C
MANE Select: NM_001012759
dbSNP: rs1058158
Type: single nucleotide variant
Location: chr16:88715206 (GRCh38)
Gene constraint: LOEUF 1.535 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.27

Full CTU2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CTU2 c.1420-1G>A Likely pathogenic ★★ same condition
CTU2 c.282+5G>A Pathogenic ★★ same condition
CTU2 p.Gln243Ter Pathogenic/Likely pathogenic ★★ same condition
CTU2 p.Thr291= Pathogenic ★★ same condition
CTU2 p.Gln416Ter Uncertain significance ★★ same condition
CTU2 c.1006-26A>G Benign ★★ same condition
CTU2 c.1201+29C>G Benign ★★ same condition
CTU2 c.1420-37A>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/ctu2-p-arg501 (accessed [today's date]).

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